diff --git a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/VcsLogHashMapImpl.java b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/VcsLogHashMapImpl.java
index ba163341ef09..6943d18531b0 100644
--- a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/VcsLogHashMapImpl.java
+++ b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/VcsLogHashMapImpl.java
@@ -74,6 +74,9 @@ public class VcsLogHashMapImpl implements Disposable, VcsLogHashMap {
   @NotNull private static final Logger LOG = Logger.getInstance(VcsLogHashMap.class);
   @NotNull private static final String LOG_KIND = "hashes";
   private static final int VERSION = 3;
+  @NotNull private static final String ROOT_STORAGE_KIND = "roots";
+  private static final int ROOTS_STORAGE_VERSION = 0;
+
   private static final int NO_INDEX = -1;
 
   @NotNull private final PersistentEnumerator<CommitId> myPersistentEnumerator;
@@ -91,9 +94,14 @@ public class VcsLogHashMapImpl implements Disposable, VcsLogHashMap {
     myPersistentEnumerator = PersistentUtil.createPersistentEnumerator(new MyCommitIdKeyDescriptor(roots), LOG_KIND,
                                                                        PersistentUtil.calcLogId(project, logProviders), VERSION);
 
+    // cleanup old root storages, to remove after 2016.3 release
+    PersistentUtil
+      .cleanupOldStorageFile(project.getName() + "." + project.getBaseDir().getPath().hashCode(), ROOT_STORAGE_KIND, ROOTS_STORAGE_VERSION);
+
     Disposer.register(parent, this);
   }
 
+
   @Nullable
   private CommitId doGetCommitId(int index) throws IOException {
     return myPersistentEnumerator.valueOf(index);
diff --git a/platform/vcs-log/impl/src/com/intellij/vcs/log/util/PersistentUtil.java b/platform/vcs-log/impl/src/com/intellij/vcs/log/util/PersistentUtil.java
index fe54d8929437..a04c52c30692 100644
--- a/platform/vcs-log/impl/src/com/intellij/vcs/log/util/PersistentUtil.java
+++ b/platform/vcs-log/impl/src/com/intellij/vcs/log/util/PersistentUtil.java
@@ -55,6 +55,10 @@ public class PersistentUtil {
     return mapFile;
   }
 
+  public static void cleanupOldStorageFile(@NotNull String logId, @NotNull String logKind, int version) {
+    IOUtil.deleteAllFilesStartingWith(getStorageFile(logId, logKind, version));
+  }
+
   @NotNull
   public static <T> PersistentEnumerator<T> createPersistentEnumerator(@NotNull final KeyDescriptor<T> keyDescriptor,
                                                                        @NotNull String logKind,