diff --git a/core/org.eclipse.cdt.ui.tests/ui/org/eclipse/cdt/ui/tests/refactoring/includes/IncludeOrganizerTest.java b/core/org.eclipse.cdt.ui.tests/ui/org/eclipse/cdt/ui/tests/refactoring/includes/IncludeOrganizerTest.java
index 016a537f009..e3086ee9136 100644
--- a/core/org.eclipse.cdt.ui.tests/ui/org/eclipse/cdt/ui/tests/refactoring/includes/IncludeOrganizerTest.java
+++ b/core/org.eclipse.cdt.ui.tests/ui/org/eclipse/cdt/ui/tests/refactoring/includes/IncludeOrganizerTest.java
@@ -24,7 +24,9 @@ import org.eclipse.text.edits.TextEdit;
 import org.eclipse.cdt.core.model.ITranslationUnit;
 import org.eclipse.cdt.ui.PreferenceConstants;
 
+import org.eclipse.cdt.internal.ui.refactoring.includes.HeaderSubstitutionMap;
 import org.eclipse.cdt.internal.ui.refactoring.includes.IHeaderChooser;
+import org.eclipse.cdt.internal.ui.refactoring.includes.IncludeMap;
 import org.eclipse.cdt.internal.ui.refactoring.includes.IncludeOrganizer;
 import org.eclipse.cdt.internal.ui.refactoring.includes.IncludePreferences;
 import org.eclipse.cdt.internal.ui.refactoring.includes.IncludePreferences.UnusedStatementDisposition;
@@ -58,6 +60,7 @@ public class IncludeOrganizerTest extends IncludesTestBase {
 		preferenceStore.setToDefault(PreferenceConstants.FORWARD_DECLARE_TEMPLATES);
 		preferenceStore.setToDefault(PreferenceConstants.FORWARD_DECLARE_NAMESPACE_ELEMENTS);
 		preferenceStore.setToDefault(PreferenceConstants.INCLUDES_ALLOW_REORDERING);
+		preferenceStore.setToDefault(IncludePreferences.INCLUDES_HEADER_SUBSTITUTION);
 		preferenceStore.setToDefault(IncludePreferences.INCLUDES_SYMBOL_EXPORTING_HEADERS);
 	}
 
@@ -338,6 +341,33 @@ public class IncludeOrganizerTest extends IncludesTestBase {
 		assertExpectedResults();
 	}
 
+	//h1.h
+	//class A {};
+
+	//h2.h
+	//#include "h1.h"	// IWYU pragma: export
+	//class B {};
+
+	//h3.h
+	//#include "h2.h"
+
+	//source.cpp
+	//A a;
+	//B b;
+	//====================
+	//#include "h3.h"
+	//
+	//A a;
+	//B b;
+	public void testIndirectHeaderExport() throws Exception {
+		HeaderSubstitutionMap headerMap = new HeaderSubstitutionMap("Test", false,
+				new IncludeMap(true, new String[] { "h2.h", "h3.h"}),
+				new IncludeMap(false));
+		getPreferenceStore().setValue(IncludePreferences.INCLUDES_HEADER_SUBSTITUTION,
+				HeaderSubstitutionMap.serializeMaps(Collections.singletonList(headerMap)));
+		assertExpectedResults();
+	}
+
 	//h1.h
 	//#define M2(t, p) t p
 
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeCreationContext.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeCreationContext.java
index 24a7bde4e39..7660d460d96 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeCreationContext.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeCreationContext.java
@@ -59,7 +59,7 @@ public class IncludeCreationContext extends InclusionContext {
 	}
 
     /**
-     * Removes headers that are exported by other headers that will be included
+     * Removes headers that are exported by other headers that will be included.
      */
     public void removeExportedHeaders() throws CoreException {
     	// Index files keyed by their absolute paths.
@@ -69,8 +69,14 @@ public class IncludeCreationContext extends InclusionContext {
     		filesByPath.put(path, file);
     	}
 
-    	Set<IPath> exportedHeaders = new HashSet<IPath>();
-		for (IPath path : fHeadersToInclude) {
+    	removeExportedHeaders(fHeadersAlreadyIncluded, filesByPath);
+    	removeExportedHeaders(fHeadersToInclude, filesByPath);
+    }
+
+	private void removeExportedHeaders(Set<IPath> exportingHeaders,
+			Map<IPath, IIndexFile> filesByPath) throws CoreException {
+		Set<IPath> exportedHeaders = new HashSet<IPath>();
+		for (IPath path : exportingHeaders) {
 			if (!exportedHeaders.contains(path)) {
 				IIndexFile file = filesByPath.get(path);
 				if (file != null) {  // file can be null if the header was not indexed.
@@ -91,7 +97,7 @@ public class IncludeCreationContext extends InclusionContext {
 			}
 		}
 		fHeadersToInclude.removeAll(exportedHeaders);
-    }
+	}
 
 	private static IPath getPath(IIndexFile file) throws CoreException {
 		return IndexLocationFactory.getAbsolutePath(file.getLocation());
@@ -103,6 +109,7 @@ public class IncludeCreationContext extends InclusionContext {
 
 	public final void addHeaderToInclude(IPath header) {
 		fHeadersToInclude.add(header);
+		fHeadersAlreadyIncluded.add(header);
 	}
 
 	public final boolean isToBeIncluded(IPath header) {
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeOrganizer.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeOrganizer.java
index 2441ddc457c..8105552b2b8 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeOrganizer.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/refactoring/includes/IncludeOrganizer.java
@@ -746,6 +746,7 @@ public class IncludeOrganizer {
 			if (!request.isResolved() && !isExportedBinding(request, headerSubstitutor)) {
 				List<IPath> candidatePaths = request.getCandidatePaths();
 				Set<IPath> representativeHeaders = new HashSet<IPath>();
+				Set<IPath> representedHeaders = new HashSet<IPath>();
 				boolean allRepresented = true;
 				for (IPath path : candidatePaths) {
 					if (fContext.isIncluded(path)) {
@@ -759,6 +760,7 @@ public class IncludeOrganizer {
 						IPath header = headerSubstitutor.getUniqueRepresentativeHeader(path);
 						if (header != null) {
 							representativeHeaders.add(header);
+							representedHeaders.add(path);
 						} else {
 							allRepresented = false;
 						}
@@ -772,6 +774,10 @@ public class IncludeOrganizer {
 						System.out.println(request.toString() + " (unique representative)"); //$NON-NLS-1$
 					if (!fContext.isAlreadyIncluded(path))
 						fContext.addHeaderToInclude(path);
+					for (IPath header : representedHeaders) {
+						if (!header.equals(path))
+							fContext.addHeaderAlreadyIncluded(header);
+					}
 				}
 			}
 		}
@@ -799,6 +805,8 @@ public class IncludeOrganizer {
 						}
 						if (!fContext.isAlreadyIncluded(header))
 							fContext.addHeaderToInclude(header);
+						if (!header.equals(path))
+							fContext.addHeaderAlreadyIncluded(path);
 					}
 				}
 			}