diff --git a/apps/opencs/model/doc/saving.cpp b/apps/opencs/model/doc/saving.cpp
index 27d21635e..45b53f4fe 100644
--- a/apps/opencs/model/doc/saving.cpp
+++ b/apps/opencs/model/doc/saving.cpp
@@ -65,7 +65,11 @@ CSMDoc::Saving::Saving (Document& document, const boost::filesystem::path& proje
 
     appendStage (new WriteRefIdCollectionStage (mDocument, mState));
 
+    appendStage (new CollectionReferencesStage (mDocument, mState));
 
+    appendStage (new WriteCellCollectionStage (mDocument, mState));
+
+    // close file and clean up
     appendStage (new CloseSaveStage (mState));
 
     appendStage (new FinalSavingStage (mDocument, mState));
diff --git a/apps/opencs/model/doc/savingstages.cpp b/apps/opencs/model/doc/savingstages.cpp
index 066c76734..d36c2fb86 100644
--- a/apps/opencs/model/doc/savingstages.cpp
+++ b/apps/opencs/model/doc/savingstages.cpp
@@ -9,6 +9,8 @@
 
 #include <components/esm/loaddial.hpp>
 
+#include <components/misc/stringops.hpp>
+
 #include "../world/infocollection.hpp"
 
 #include "document.hpp"
@@ -216,6 +218,143 @@ void CSMDoc::WriteFilterStage::perform (int stage, Messages& messages)
 }
 
 
+CSMDoc::CollectionReferencesStage::CollectionReferencesStage (Document& document,
+    SavingState& state)
+: mDocument (document), mState (state)
+{}
+
+int CSMDoc::CollectionReferencesStage::setup()
+{
+    mState.getSubRecords().clear();
+
+    int size = mDocument.getData().getReferences().getSize();
+
+    int steps = size/100;
+    if (size%100) ++steps;
+
+    return steps;
+}
+
+void CSMDoc::CollectionReferencesStage::perform (int stage, Messages& messages)
+{
+    int size = mDocument.getData().getReferences().getSize();
+
+    for (int i=stage*100; i<stage*100+100 && i<size; ++i)
+    {
+        const CSMWorld::Record<CSMWorld::CellRef>& record =
+            mDocument.getData().getReferences().getRecord (i);
+
+        if (record.mState==CSMWorld::RecordBase::State_Deleted ||
+            record.mState==CSMWorld::RecordBase::State_Modified ||
+            record.mState==CSMWorld::RecordBase::State_ModifiedOnly)
+        {
+            mState.getSubRecords()[Misc::StringUtils::lowerCase (record.get().mCell)]
+                .push_back (i);
+        }
+    }
+}
+
+
+CSMDoc::WriteCellCollectionStage::WriteCellCollectionStage (Document& document,
+    SavingState& state)
+: mDocument (document), mState (state)
+{}
+
+int CSMDoc::WriteCellCollectionStage::setup()
+{
+    return mDocument.getData().getCells().getSize();
+}
+
+void CSMDoc::WriteCellCollectionStage::perform (int stage, Messages& messages)
+{
+    const CSMWorld::Record<CSMWorld::Cell>& cell =
+        mDocument.getData().getCells().getRecord (stage);
+
+    std::map<std::string, std::vector<int> >::const_iterator references =
+        mState.getSubRecords().find (Misc::StringUtils::lowerCase (cell.get().mId));
+
+    if (cell.mState==CSMWorld::RecordBase::State_Modified ||
+        cell.mState==CSMWorld::RecordBase::State_ModifiedOnly ||
+        references!=mState.getSubRecords().end())
+    {
+        bool interior = cell.get().mId.substr (0, 1)!="#";
+
+        // write cell data
+        mState.getWriter().startRecord (cell.mModified.sRecordId);
+
+        mState.getWriter().writeHNOCString ("NAME", cell.get().mName);
+
+        ESM::Cell cell2 = cell.get();
+
+        if (interior)
+            cell2.mData.mFlags |= ESM::Cell::Interior;
+        else
+        {
+            cell2.mData.mFlags &= ~ESM::Cell::Interior;
+
+            std::istringstream stream (cell.get().mId.c_str());
+            char ignore;
+            stream >> ignore >> cell2.mData.mX >> cell2.mData.mY;
+        }
+        cell2.save (mState.getWriter());
+
+        // write references
+        if (references!=mState.getSubRecords().end())
+        {
+            // first pass: find highest RefNum
+            int lastRefNum = -1;
+
+            for (std::vector<int>::const_iterator iter (references->second.begin());
+                iter!=references->second.end(); ++iter)
+            {
+                const CSMWorld::Record<CSMWorld::CellRef>& ref =
+                    mDocument.getData().getReferences().getRecord (*iter);
+
+                if (ref.get().mRefNum.mContentFile==0 && ref.get().mRefNum.mIndex>lastRefNum)
+                    lastRefNum = ref.get().mRefNum.mIndex;
+            }
+
+            // second pass: write
+            for (std::vector<int>::const_iterator iter (references->second.begin());
+                iter!=references->second.end(); ++iter)
+            {
+                const CSMWorld::Record<CSMWorld::CellRef>& ref =
+                    mDocument.getData().getReferences().getRecord (*iter);
+
+                if (ref.mState==CSMWorld::RecordBase::State_Modified ||
+                    ref.mState==CSMWorld::RecordBase::State_ModifiedOnly)
+                {
+                    if (ref.get().mRefNum.mContentFile==-2)
+                    {
+                        if (lastRefNum>=0xffffff)
+                            throw std::runtime_error (
+                                "RefNums exhausted in cell: " + cell.get().mId);
+
+                        ESM::CellRef ref2 = ref.get();
+                        ref2.mRefNum.mContentFile = 0;
+                        ref2.mRefNum.mIndex = ++lastRefNum;
+
+                        ref2.save (mState.getWriter());
+                    }
+                    else
+                        ref.get().save (mState.getWriter());
+                }
+                else if (ref.mState==CSMWorld::RecordBase::State_Deleted)
+                {
+                    /// \todo write record with delete flag
+                }
+            }
+        }
+
+        mState.getWriter().endRecord (cell.mModified.sRecordId);
+    }
+    else if (cell.mState==CSMWorld::RecordBase::State_Deleted)
+    {
+        /// \todo write record with delete flag
+    }
+}
+
+
 CSMDoc::CloseSaveStage::CloseSaveStage (SavingState& state)
 : mState (state)
 {}
diff --git a/apps/opencs/model/doc/savingstages.hpp b/apps/opencs/model/doc/savingstages.hpp
index c2f0a150a..dcb1a8650 100644
--- a/apps/opencs/model/doc/savingstages.hpp
+++ b/apps/opencs/model/doc/savingstages.hpp
@@ -161,10 +161,42 @@ namespace CSMDoc
 
             WriteFilterStage (Document& document, SavingState& state, CSMFilter::Filter::Scope scope);
 
+            virtual void perform (int stage, Messages& messages);
+            ///< Messages resulting from this stage will be appended to \a messages.
+
+    };
+
+    class CollectionReferencesStage : public Stage
+    {
+            Document& mDocument;
+            SavingState& mState;
+
+        public:
+
+            CollectionReferencesStage (Document& document, SavingState& state);
+
+            virtual int setup();
+            ///< \return number of steps
+
             virtual void perform (int stage, Messages& messages);
             ///< Messages resulting from this stage will be appended to \a messages.
     };
 
+    class WriteCellCollectionStage : public Stage
+    {
+            Document& mDocument;
+            SavingState& mState;
+
+        public:
+
+            WriteCellCollectionStage (Document& document, SavingState& state);
+
+            virtual int setup();
+            ///< \return number of steps
+
+            virtual void perform (int stage, Messages& messages);
+            ///< Messages resulting from this stage will be appended to \a messages.
+    };
 
     class CloseSaveStage : public Stage
     {
diff --git a/apps/opencs/model/doc/savingstate.cpp b/apps/opencs/model/doc/savingstate.cpp
index 07c42a490..84bca1e95 100644
--- a/apps/opencs/model/doc/savingstate.cpp
+++ b/apps/opencs/model/doc/savingstate.cpp
@@ -25,6 +25,8 @@ void CSMDoc::SavingState::start (Document& document, bool project)
 
     mStream.clear();
 
+    mSubRecords.clear();
+
     if (project)
         mPath = mProjectPath;
     else
@@ -61,3 +63,8 @@ bool CSMDoc::SavingState::isProjectFile() const
 {
     return mProjectFile;
 }
+
+std::map<std::string, std::vector<int> >& CSMDoc::SavingState::getSubRecords()
+{
+    return mSubRecords;
+}
diff --git a/apps/opencs/model/doc/savingstate.hpp b/apps/opencs/model/doc/savingstate.hpp
index 7b0c37386..577fc734d 100644
--- a/apps/opencs/model/doc/savingstate.hpp
+++ b/apps/opencs/model/doc/savingstate.hpp
@@ -2,6 +2,7 @@
 #define CSM_DOC_SAVINGSTATE_H
 
 #include <fstream>
+#include <map>
 
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/fstream.hpp>
@@ -25,6 +26,7 @@ namespace CSMDoc
             ESM::ESMWriter mWriter;
             boost::filesystem::path mProjectPath;
             bool mProjectFile;
+            std::map<std::string, std::vector<int> > mSubRecords; // record ID, list of subrecords
 
         public:
 
@@ -46,6 +48,8 @@ namespace CSMDoc
 
             bool isProjectFile() const;
             ///< Currently saving project file? (instead of content file)
+
+            std::map<std::string, std::vector<int> >& getSubRecords();
     };
 
 
diff --git a/apps/opencs/model/world/cell.cpp b/apps/opencs/model/world/cell.cpp
index cd58fca1e..40520a9ba 100644
--- a/apps/opencs/model/world/cell.cpp
+++ b/apps/opencs/model/world/cell.cpp
@@ -18,8 +18,3 @@ void CSMWorld::Cell::load (ESM::ESMReader &esm)
         mId = stream.str();
     }
 }
-
-void CSMWorld::Cell::addRef (const std::string& id)
-{
-    mRefs.push_back (std::make_pair (id, false));
-}
\ No newline at end of file
diff --git a/apps/opencs/model/world/cell.hpp b/apps/opencs/model/world/cell.hpp
index e6f3c8c35..8a2781590 100644
--- a/apps/opencs/model/world/cell.hpp
+++ b/apps/opencs/model/world/cell.hpp
@@ -1,7 +1,7 @@
 #ifndef CSM_WOLRD_CELL_H
 #define CSM_WOLRD_CELL_H
 
-#include <vector>
+#include <set>
 #include <string>
 
 #include <components/esm/loadcell.hpp>
@@ -15,12 +15,12 @@ namespace CSMWorld
     struct Cell : public ESM::Cell
     {
         std::string mId;
-        std::vector<std::pair<std::string, bool> > mRefs; // ID, modified
-        std::vector<std::string> mDeletedRefs;
 
-        void load (ESM::ESMReader &esm);
+        /// These are the references modified by the edited content file. These are stored in
+        /// mModified only.
+        std::set<std::string> mTouchedRefs;
 
-        void addRef (const std::string& id);
+        void load (ESM::ESMReader &esm);
     };
 }
 
diff --git a/apps/opencs/model/world/columnimp.hpp b/apps/opencs/model/world/columnimp.hpp
index 6976b454d..6b276d151 100644
--- a/apps/opencs/model/world/columnimp.hpp
+++ b/apps/opencs/model/world/columnimp.hpp
@@ -10,6 +10,7 @@
 #include "columnbase.hpp"
 #include "columns.hpp"
 #include "info.hpp"
+#include "cell.hpp"
 
 namespace CSMWorld
 {
@@ -87,6 +88,45 @@ namespace CSMWorld
         }
     };
 
+    /// \brief Specialisation that takes care of the modified reference tracking
+    template<>
+    struct RecordStateColumn<Cell> : public Column<Cell>
+    {
+        RecordStateColumn<Cell>()
+        : Column<Cell> (Columns::ColumnId_Modification, ColumnBase::Display_RecordState)
+        {}
+
+        virtual QVariant get (const Record<Cell>& record) const
+        {
+            if (record.mState==Record<Cell>::State_Erased)
+                return static_cast<int> (Record<Cell>::State_Deleted);
+
+            if (!record.mModified.mTouchedRefs.empty() &&
+                !record.mState==Record<Cell>::State_Deleted &&
+                !record.mState==Record<Cell>::State_ModifiedOnly)
+            {
+                static_cast<int> (Record<Cell>::State_Modified);
+            }
+
+            return static_cast<int> (record.mState);
+        }
+
+        virtual void set (Record<Cell>& record, const QVariant& data)
+        {
+            record.mState = static_cast<RecordBase::State> (data.toInt());
+        }
+
+        virtual bool isEditable() const
+        {
+            return true;
+        }
+
+        virtual bool isUserEditable() const
+        {
+            return false;
+        }
+    };
+
     template<typename ESXRecordT>
     struct FixedRecordTypeColumn : public Column<ESXRecordT>
     {
diff --git a/apps/opencs/model/world/data.cpp b/apps/opencs/model/world/data.cpp
index ff33b4665..442e73e51 100644
--- a/apps/opencs/model/world/data.cpp
+++ b/apps/opencs/model/world/data.cpp
@@ -489,6 +489,7 @@ int CSMWorld::Data::startLoading (const boost::filesystem::path& path, bool base
     delete mReader;
     mReader = 0;
     mDialogue = 0;
+    mRefLoadCache.clear();
 
     mReader = new ESM::ESMReader;
     mReader->setEncoder (&mEncoder);
@@ -513,6 +514,7 @@ bool CSMWorld::Data::continueLoading (CSMDoc::Stage::Messages& messages)
         delete mReader;
         mReader = 0;
         mDialogue = 0;
+        mRefLoadCache.clear();
         return true;
     }
 
@@ -534,9 +536,12 @@ bool CSMWorld::Data::continueLoading (CSMDoc::Stage::Messages& messages)
         case ESM::REC_SPEL: mSpells.load (*mReader, mBase); break;
 
         case ESM::REC_CELL:
+        {
             mCells.load (*mReader, mBase);
-            mRefs.load (*mReader, mCells.getSize()-1, mBase);
+            std::string cellId = Misc::StringUtils::lowerCase (mCells.getId (mCells.getSize()-1));
+            mRefs.load (*mReader, mCells.getSize()-1, mBase, mRefLoadCache[cellId], messages);
             break;
+        }
 
         case ESM::REC_ACTI: mReferenceables.load (*mReader, mBase, UniversalId::Type_Activator); break;
         case ESM::REC_ALCH: mReferenceables.load (*mReader, mBase, UniversalId::Type_Potion); break;
diff --git a/apps/opencs/model/world/data.hpp b/apps/opencs/model/world/data.hpp
index ab247b6a3..9a842878a 100644
--- a/apps/opencs/model/world/data.hpp
+++ b/apps/opencs/model/world/data.hpp
@@ -77,6 +77,7 @@ namespace CSMWorld
             const ESM::Dialogue *mDialogue; // last loaded dialogue
             bool mBase;
             bool mProject;
+            std::map<std::string, std::map<ESM::RefNum, std::string> > mRefLoadCache;
 
             // not implemented
             Data (const Data&);
diff --git a/apps/opencs/model/world/ref.cpp b/apps/opencs/model/world/ref.cpp
index cf9e496ee..d1bd771f8 100644
--- a/apps/opencs/model/world/ref.cpp
+++ b/apps/opencs/model/world/ref.cpp
@@ -1,12 +1,10 @@
 
 #include "ref.hpp"
 
-#include "cell.hpp"
-
-void CSMWorld::CellRef::load (ESM::ESMReader &esm, Cell& cell, const std::string& id)
+CSMWorld::CellRef::CellRef()
 {
-    mId = id;
-    mCell = cell.mId;
+    mRefNum.mIndex = 0;
 
-    cell.addRef (mId);
+    // special marker: This reference does not have a RefNum assign to it yet.
+    mRefNum.mContentFile = -2;
 }
\ No newline at end of file
diff --git a/apps/opencs/model/world/ref.hpp b/apps/opencs/model/world/ref.hpp
index fcf016ee2..eb62434cf 100644
--- a/apps/opencs/model/world/ref.hpp
+++ b/apps/opencs/model/world/ref.hpp
@@ -3,11 +3,6 @@
 
 #include <components/esm/cellref.hpp>
 
-namespace ESM
-{
-    class ESMReader;
-}
-
 namespace CSMWorld
 {
     class Cell;
@@ -18,8 +13,7 @@ namespace CSMWorld
         std::string mId;
         std::string mCell;
 
-        void load (ESM::ESMReader &esm, Cell& cell, const std::string& id);
-        ///< Load cell ref and register it with \a cell.
+        CellRef();
     };
 }
 
diff --git a/apps/opencs/model/world/refcollection.cpp b/apps/opencs/model/world/refcollection.cpp
index 4fdd97909..36518f0fa 100644
--- a/apps/opencs/model/world/refcollection.cpp
+++ b/apps/opencs/model/world/refcollection.cpp
@@ -3,12 +3,15 @@
 
 #include <sstream>
 
+#include <components/misc/stringops.hpp>
+
 #include "ref.hpp"
 #include "cell.hpp"
 #include "universalid.hpp"
 #include "record.hpp"
 
-void CSMWorld::RefCollection::load (ESM::ESMReader& reader, int cellIndex, bool base)
+void CSMWorld::RefCollection::load (ESM::ESMReader& reader, int cellIndex, bool base,
+    std::map<ESM::RefNum, std::string>& cache, CSMDoc::Stage::Messages& messages)
 {
     Record<Cell> cell = mCells.getRecord (cellIndex);
 
@@ -17,19 +20,79 @@ void CSMWorld::RefCollection::load (ESM::ESMReader& reader, int cellIndex, bool
     CellRef ref;
 
     bool deleted = false;
-    while (cell2.getNextRef (reader, ref, deleted))
+
+    while (ESM::Cell::getNextRef (reader, ref, deleted))
     {
-        /// \todo handle deleted and moved references
-        ref.load (reader, cell2, getNewId());
+        ref.mCell = cell2.mId;
 
-        Record<CellRef> record2;
-        record2.mState = base ? RecordBase::State_BaseOnly : RecordBase::State_ModifiedOnly;
-        (base ? record2.mBase : record2.mModified) = ref;
+        /// \todo handle moved references
 
-        appendRecord (record2);
-    }
+        std::map<ESM::RefNum, std::string>::iterator iter = cache.find (ref.mRefNum);
+
+        if (deleted)
+        {
+            if (iter==cache.end())
+            {
+                CSMWorld::UniversalId id (CSMWorld::UniversalId::Type_Cell,
+                    mCells.getId (cellIndex));
+
+                messages.push_back (std::make_pair (id,
+                    "Attempt to delete a non-existing reference"));
+
+                continue;
+            }
+
+            int index = getIndex (iter->second);
+
+            Record<CellRef> record = getRecord (index);
+
+            if (record.mState==RecordBase::State_BaseOnly)
+            {
+                removeRows (index, 1);
+                cache.erase (iter);
+            }
+            else
+            {
+                cell.mModified.mTouchedRefs.insert (Misc::StringUtils::lowerCase (
+                    mCells.getId (cellIndex)));
+                record.mState = RecordBase::State_Deleted;
+                setRecord (index, record);
+            }
 
-    mCells.setRecord (cellIndex, cell);
+            continue;
+        }
+
+        if (!base)
+            cell.mModified.mTouchedRefs.insert (Misc::StringUtils::lowerCase (
+                mCells.getId (cellIndex)));
+
+        if (iter==cache.end())
+        {
+            // new reference
+            ref.mId = getNewId();
+
+            Record<CellRef> record;
+            record.mState = base ? RecordBase::State_BaseOnly : RecordBase::State_ModifiedOnly;
+            (base ? record.mBase : record.mModified) = ref;
+
+            appendRecord (record);
+
+            cache.insert (std::make_pair (ref.mRefNum, ref.mId));
+        }
+        else
+        {
+            // old reference -> merge
+            ref.mId = iter->second;
+
+            int index = getIndex (ref.mId);
+
+            Record<CellRef> record = getRecord (index);
+            record.mState = base ? RecordBase::State_BaseOnly : RecordBase::State_Modified;
+            (base ? record.mBase : record.mModified) = ref;
+
+            setRecord (index, record);
+        }
+    }
 }
 
 std::string CSMWorld::RefCollection::getNewId()
diff --git a/apps/opencs/model/world/refcollection.hpp b/apps/opencs/model/world/refcollection.hpp
index 173efba05..63d369ed9 100644
--- a/apps/opencs/model/world/refcollection.hpp
+++ b/apps/opencs/model/world/refcollection.hpp
@@ -1,6 +1,10 @@
 #ifndef CSM_WOLRD_REFCOLLECTION_H
 #define CSM_WOLRD_REFCOLLECTION_H
 
+#include <map>
+
+#include "../doc/stage.hpp"
+
 #include "collection.hpp"
 #include "ref.hpp"
 #include "record.hpp"
@@ -22,7 +26,9 @@ namespace CSMWorld
               : mCells (cells), mNextId (0)
             {}
 
-            void load (ESM::ESMReader& reader, int cellIndex, bool base);
+            void load (ESM::ESMReader& reader, int cellIndex, bool base,
+                std::map<ESM::RefNum, std::string>& cache,
+                CSMDoc::Stage::Messages& messages);
             ///< Load a sequence of references.
 
             std::string getNewId();
diff --git a/components/esm/cellref.cpp b/components/esm/cellref.cpp
index 84518bed9..d785fb2b6 100644
--- a/components/esm/cellref.cpp
+++ b/components/esm/cellref.cpp
@@ -172,3 +172,14 @@ bool ESM::operator== (const RefNum& left, const RefNum& right)
 {
     return left.mIndex==right.mIndex && left.mContentFile==right.mContentFile;
 }
+
+bool ESM::operator< (const RefNum& left, const RefNum& right)
+{
+    if (left.mIndex<right.mIndex)
+        return true;
+
+    if (left.mIndex>right.mIndex)
+        return false;
+
+    return left.mContentFile<right.mContentFile;
+}
diff --git a/components/esm/cellref.hpp b/components/esm/cellref.hpp
index 5f53eadbe..b87578120 100644
--- a/components/esm/cellref.hpp
+++ b/components/esm/cellref.hpp
@@ -99,6 +99,7 @@ namespace ESM
     };
 
     bool operator== (const RefNum& left, const RefNum& right);
+    bool operator< (const RefNum& left, const RefNum& right);
 }
 
 #endif