diff --git a/core/org.eclipse.cdt.core/index/org/eclipse/cdt/internal/core/index/ctagsindexer/CTagsIndexAll.java b/core/org.eclipse.cdt.core/index/org/eclipse/cdt/internal/core/index/ctagsindexer/CTagsIndexAll.java
index 52e56d6425c..8b750e34bda 100644
--- a/core/org.eclipse.cdt.core/index/org/eclipse/cdt/internal/core/index/ctagsindexer/CTagsIndexAll.java
+++ b/core/org.eclipse.cdt.core/index/org/eclipse/cdt/internal/core/index/ctagsindexer/CTagsIndexAll.java
@@ -12,6 +12,8 @@ package org.eclipse.cdt.internal.core.index.ctagsindexer;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.HashSet;
+import java.util.Iterator;
 
 import org.eclipse.cdt.core.CCorePlugin;
 import org.eclipse.cdt.core.CommandLauncher;
@@ -24,6 +26,7 @@ import org.eclipse.cdt.core.model.ICProject;
 import org.eclipse.cdt.core.model.IIncludeReference;
 import org.eclipse.cdt.internal.core.index.IIndex;
 import org.eclipse.cdt.internal.core.index.cindexstorage.CIndexStorage;
+import org.eclipse.cdt.internal.core.index.cindexstorage.Util;
 import org.eclipse.cdt.internal.core.index.domsourceindexer.AbstractIndexerRunner;
 import org.eclipse.cdt.internal.core.search.indexing.IndexManager;
 import org.eclipse.cdt.internal.core.search.indexing.ReadWriteMonitor;
@@ -123,7 +126,8 @@ class CTagsIndexAll extends CTagsIndexRequest {
 			 }
 			 
 			 //Try to index includes (if any exist)
-			 //cTagsInclude(index);
+			 if (ctagIndexIncludes())
+				 cTagsInclude(index);
 				 
 		} catch (IOException e) {
 			if (IndexManager.VERBOSE) {
@@ -146,20 +150,58 @@ class CTagsIndexAll extends CTagsIndexRequest {
 			refs = cProj.getIncludeReferences();
 		} catch (CModelException e) {}
 		
+		
+		//Find common base for references
+		String[] pathString = new String[refs.length];
 		for (int i=0; i<refs.length; i++){
-		  	runCTags(refs[i].getPath());
+			pathString[i] = refs[i].getPath().toOSString();
+		}
+		Util.sort(pathString);
+		
+		HashSet finalArray = new HashSet();
+		String currentString = null;
+		for (int i=0; i<refs.length; i++){
+			if (currentString == null){
+				currentString = pathString[i];
+				finalArray.add(currentString);
+			} else {
+				if (pathString[i].startsWith(currentString)){
+					continue;
+				} else {
+					currentString = pathString[i];
+					finalArray.add(currentString);
+				}
+			}
+		}
+		finalArray.add(currentString);
+		
+		Iterator iter = finalArray.iterator();
+		
+		while (iter.hasNext()) {
+			IPath newPath = new Path((String) iter.next());
+			runCTags(newPath);
 		  	ctagsFileToUse=ctagsFile;
 			 //Parse the CTag File
 		     CTagsFileReader reader = new CTagsFileReader(project,ctagsFileToUse,indexer);
-		     reader.setRootDirectory(refs[i].getPath());
+		     reader.setRootDirectory(newPath);
 		     reader.setIndex(index);
 		     reader.parse();
 		}
-		
 	     // request to save index when all cus have been indexed
 	     indexer.request(new CTagsSaveIndex(this.indexPath, indexer));
 	}
 
+	private void sortPathArray(IPath[] paths) {
+		
+		if (paths.length <= 1)
+			return;
+		
+		for (int i=0; i<paths.length; i++){
+			
+		}
+		
+	}
+
 	/**
      * @return
      */
@@ -237,6 +279,27 @@ class CTagsIndexAll extends CTagsIndexRequest {
 		return false;
 	}
 	
+	private boolean ctagIndexIncludes(){
+		try {
+			ICDescriptor cdesc = CCorePlugin.getDefault().getCProjectDescription(project, false);
+			if (cdesc == null)
+				return true;
+			
+			ICExtensionReference[] cext = cdesc.get(CCorePlugin.INDEXER_UNIQ_ID);
+			if (cext.length > 0) {
+				for (int i = 0; i < cext.length; i++) {
+					String id = cext[i].getID();
+						String orig = cext[i].getExtensionData("ctagsindexincludes"); //$NON-NLS-1$
+						if (orig != null){
+							return new Boolean(orig).booleanValue();
+						}
+				}
+			}
+		} catch (CoreException e) {}
+		
+		return false;
+	}
+	
 	private boolean getCTagsFileLocation() {
 		try {
 			ICDescriptor cdesc = CCorePlugin.getDefault().getCProjectDescription(project, false);
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/CUIMessages.properties b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/CUIMessages.properties
index 344205d03e6..cc751c0905e 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/CUIMessages.properties
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/CUIMessages.properties
@@ -71,6 +71,9 @@ CTagsIndexerBlock.radioButtonExternal=Import existing CTags file
 CTagsIndexerBlock.browseButton=Browse...
 CTagsIndexerBlock.fileBrowser=Select CTags File
 
+CTagsIndexerBlock.includeGroup=Include Files
+CTagsIndexerBlock.indexIncludes=Index include paths
+
 StatusBarUpdater.num_elements_selected={0} items selected
 
 CElementLabels.anonymous=(anon)
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/dialogs/CTagsIndexerBlock.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/dialogs/CTagsIndexerBlock.java
index 447ce713a2d..34a68669087 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/dialogs/CTagsIndexerBlock.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/dialogs/CTagsIndexerBlock.java
@@ -43,14 +43,17 @@ public class CTagsIndexerBlock extends AbstractIndexerPage {
     protected boolean externalTagsFile = false;
     protected Button internalCTagsFile;
     protected Button externalCTagsFile;
+    protected Button indexIncludePaths;
 	protected Button browseButton;
 	protected Text cTagsFile;
 	
+	
 	private String storedInternalExternal;
 	private String storedTagFile;
 	
 	public final static String PREF_INTOREXT_CTAGS = CUIPlugin.PLUGIN_ID + ".intorextctags"; //$NON-NLS-1$
 	public final static String PREF_CTAGSLOCATION_CTAGS = CUIPlugin.PLUGIN_ID + ".ctagslocation"; //$NON-NLS-1$
+	public final static String PREF_CTAGS_INDEXINCLUDEFILES = CUIPlugin.PLUGIN_ID + ".ctagsindexincludes"; //$NON-NLS-1$
 	
     /* (non-Javadoc)
      * @see org.eclipse.cdt.ui.index.AbstractIndexerPage#initialize(org.eclipse.core.resources.IProject)
@@ -75,7 +78,8 @@ public class CTagsIndexerBlock extends AbstractIndexerPage {
 			IProject proj = null;
 	        String internalExternalCTagsString = internalTagsFile ? CTagsIndexer.CTAGS_INTERNAL  : CTagsIndexer.CTAGS_EXTERNAL;
 			String cTagsFileLocation = cTagsFile.getText();
-
+			String indexIncludeFiles = new Boolean(indexIncludePaths.getSelection()).toString();
+			
 			//if external has been chosen, ensure that there is a cTagsFileLocation selected; otherwise default
 			//to internal file
 			if (internalExternalCTagsString.equals(CTagsIndexer.CTAGS_EXTERNAL) && cTagsFileLocation.equals("")) //$NON-NLS-1$
@@ -102,12 +106,17 @@ public class CTagsIndexerBlock extends AbstractIndexerPage {
 						if (orig == null || !orig.equals(cTagsFileLocation)) {
 							cext[i].setExtensionData("ctagfilelocation", cTagsFileLocation); //$NON-NLS-1$
 						}
+						orig = cext[i].getExtensionData("ctagsindexincludes"); //$NON-NLS-1$
+						if (orig == null || !orig.equals(cTagsFileLocation)) {
+							cext[i].setExtensionData("ctagsindexincludes", indexIncludeFiles); //$NON-NLS-1$
+						}
 					}
 				}
 			} else {
 				if (prefStore != null) {
 					prefStore.setValue(PREF_INTOREXT_CTAGS, internalExternalCTagsString);
 					prefStore.setValue(PREF_CTAGSLOCATION_CTAGS,cTagsFileLocation);
+					prefStore.setValue(PREF_CTAGS_INDEXINCLUDEFILES,indexIncludeFiles);
 				}
 			}
 		}
@@ -128,6 +137,15 @@ public class CTagsIndexerBlock extends AbstractIndexerPage {
     public void createControl(Composite parent) {
         Composite page = ControlFactory.createComposite(parent, 1);	
 		
+        Group includeGroup = ControlFactory.createGroup(page,CUIMessages.getString("CTagsIndexerBlock.includeGroup"),1);
+        GridData gd2 = (GridData) includeGroup.getLayoutData();
+        gd2.grabExcessHorizontalSpace = true;
+        gd2.horizontalAlignment = GridData.FILL;
+       
+        indexIncludePaths = ControlFactory.createCheckBox(includeGroup,CUIMessages.getString("CTagsIndexerBlock.indexIncludes"));//$NON-NLS-1$ //$NON-NLS-2$
+		((GridData)indexIncludePaths.getLayoutData()).horizontalSpan =1;
+		((GridData)indexIncludePaths.getLayoutData()).grabExcessHorizontalSpace = true;
+    
 		Group group = ControlFactory.createGroup(page, CUIMessages.getString("CTagsIndexerBlock.blockName"),3); //$NON-NLS-1$
         
         GridData gd = (GridData) group.getLayoutData();
@@ -204,6 +222,14 @@ public class CTagsIndexerBlock extends AbstractIndexerPage {
 					cTagsFile.setText(orig);
 				}
 				
+				orig = cext[i].getExtensionData("ctagsindexincludes"); //$NON-NLS-1$
+				if (orig != null){
+					if (new Boolean(orig).booleanValue()){
+						indexIncludePaths.setSelection(true);
+					} else {
+						indexIncludePaths.setSelection(false);
+					}
+				}
 			}
 		}