diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMManager.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMManager.java
index 13dbeb38268..1ca4bd01953 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMManager.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/PDOMManager.java
@@ -211,6 +211,9 @@ public class PDOMManager implements IWritableIndexManager, IListener {
 
 	public Job startup() {
 		fInShutDown= false;
+		// Set path canonicalization strategy early on to avoid a race condition.
+		updatePathCanonicalizationStrategy();
+
 		Job postStartupJob= new Job(CCorePlugin.getResourceString("CCorePlugin.startupJob")) { //$NON-NLS-1$
 			@Override
 			protected IStatus run(IProgressMonitor monitor) {