diff --git a/refactoring.java/src/org/netbeans/modules/refactoring/java/plugins/JavaWhereUsedQueryPlugin.java b/refactoring.java/src/org/netbeans/modules/refactoring/java/plugins/JavaWhereUsedQueryPlugin.java
--- a/refactoring.java/src/org/netbeans/modules/refactoring/java/plugins/JavaWhereUsedQueryPlugin.java
+++ b/refactoring.java/src/org/netbeans/modules/refactoring/java/plugins/JavaWhereUsedQueryPlugin.java
@@ -47,6 +47,7 @@
 import com.sun.source.tree.Tree;
 import com.sun.source.util.TreePath;
 import java.io.IOException;
+import java.net.URL;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicBoolean;
 import javax.lang.model.element.Element;
@@ -54,8 +55,10 @@
 import javax.lang.model.element.ExecutableElement;
 import javax.lang.model.element.Modifier;
 import javax.lang.model.element.TypeElement;
+import org.netbeans.api.annotations.common.NonNull;
 import org.netbeans.api.fileinfo.NonRecursiveFolder;
 import org.netbeans.api.java.classpath.ClassPath;
+import org.netbeans.api.java.queries.AnnotationProcessingQuery;
 import org.netbeans.api.java.source.*;
 import org.netbeans.api.java.source.ClassIndex.SearchScopeType;
 import org.netbeans.modules.refactoring.api.*;
@@ -69,6 +72,7 @@
 import org.netbeans.modules.refactoring.java.spi.JavaWhereUsedFilters.ReadWrite;
 import org.netbeans.modules.refactoring.spi.RefactoringElementsBag;
 import org.netbeans.modules.refactoring.spi.ui.FiltersDescription;
+import org.netbeans.spi.java.classpath.support.ClassPathSupport;
 import org.openide.ErrorManager;
 import org.openide.filesystems.FileObject;
 import org.openide.loaders.DataObject;
@@ -360,7 +364,9 @@
         }
         // filter out files that are not on source path
         Set<FileObject> set2 = new HashSet<>(set.size());
-        ClassPath cp = cpInfo.getClassPath(ClasspathInfo.PathKind.SOURCE);
+        final ClassPath scp = cpInfo.getClassPath(ClasspathInfo.PathKind.SOURCE);
+        final ClassPath aps = collectAnnotationProcessingGenSourceRoots(scp);
+        final ClassPath cp = ClassPathSupport.createProxyClassPath(scp, aps);
         for (FileObject fo : set) {
             if (cp.contains(fo)) {
                 set2.add(fo);
@@ -371,7 +377,17 @@
         }
         return set2;
     }
-    
+
+    @NonNull
+    private static ClassPath collectAnnotationProcessingGenSourceRoots(@NonNull final ClassPath scp) {
+        final FileObject[] srcRoots = scp.getRoots();
+        final Collection<URL> apRoots = new ArrayList<>(srcRoots.length);
+        for (FileObject srcRoot : srcRoots) {
+            apRoots.add(AnnotationProcessingQuery.getAnnotationProcessingOptions(srcRoot).sourceOutputDirectory());
+        }
+        return ClassPathSupport.createClassPath(apRoots.toArray(new URL[apRoots.size()]));
+    }
+
     private static Collection<FileObject> getImplementorsRecursive(ClassIndex idx, ClasspathInfo cpInfo, TypeElement el, AtomicBoolean cancel) {
         Set<?> implementorsAsHandles = RefactoringUtils.getImplementorsAsHandles(idx, cpInfo, el, cancel);