diff --git a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/PermanentGraphImpl.kt b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/PermanentGraphImpl.kt
index 7d8a083e9e83..7ebf26aea73d 100644
--- a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/PermanentGraphImpl.kt
+++ b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/PermanentGraphImpl.kt
@@ -163,8 +163,8 @@ class PermanentGraphImpl<CommitId : Any> private constructor(private val permane
       val idsGenerator = NotLoadedCommitsIdsGenerator<CommitId>()
       val linearGraph = PermanentLinearGraphBuilder.newInstance(graphCommits).build(idsGenerator)
       val permanentCommitsInfo = PermanentCommitsInfoImpl.newInstance(graphCommits, idsGenerator.notLoadedCommits)
-
-      val permanentGraphLayout = GraphLayoutBuilder.build(linearGraph) { nodeIndex1: Int, nodeIndex2: Int ->
+      val branchIndexes = permanentCommitsInfo.convertToNodeIds(branchesCommitId, true)
+      val permanentGraphLayout = GraphLayoutBuilder.build(linearGraph, branchIndexes) { nodeIndex1: Int, nodeIndex2: Int ->
         val commitId1 = permanentCommitsInfo.getCommitId(nodeIndex1)
         val commitId2 = permanentCommitsInfo.getCommitId(nodeIndex2)
         headCommitsComparator.compare(commitId1, commitId2)
diff --git a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/bek/BekBranchCreator.java b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/bek/BekBranchCreator.java
index b7024260d88f..202508ea40bc 100644
--- a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/bek/BekBranchCreator.java
+++ b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/facade/bek/BekBranchCreator.java
@@ -1,7 +1,6 @@
-// Copyright 2000-2019 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license that can be found in the LICENSE file.
+// Copyright 2000-2024 JetBrains s.r.o. and contributors. Use of this source code is governed by the Apache 2.0 license.
 package com.intellij.vcs.log.graph.impl.facade.bek;
 
-import com.intellij.openapi.diagnostic.Logger;
 import com.intellij.openapi.util.Pair;
 import com.intellij.vcs.log.graph.api.LinearGraph;
 import com.intellij.vcs.log.graph.impl.permanent.GraphLayoutImpl;
@@ -18,7 +17,6 @@ import static com.intellij.vcs.log.graph.utils.LinearGraphUtils.getDownNodes;
 import static com.intellij.vcs.log.graph.utils.LinearGraphUtils.getUpNodes;
 
 class BekBranchCreator {
-  private final static Logger LOG = Logger.getInstance(BekBranchCreator.class);
   @NotNull private final LinearGraph myPermanentGraph;
   @NotNull private final GraphLayoutImpl myGraphLayout;
   @NotNull private final Flags myDoneNodes;
@@ -36,6 +34,7 @@ class BekBranchCreator {
     List<BekBranch> bekBranches = new ArrayList<>();
 
     for (int headNode : myGraphLayout.getHeadNodeIndex()) {
+      if (myDoneNodes.get(headNode)) continue;
       List<Integer> nextBranch = createNextBranch(headNode);
       bekBranches.add(new BekBranch(myPermanentGraph, nextBranch));
     }
@@ -43,10 +42,8 @@ class BekBranchCreator {
   }
 
   public List<Integer> createNextBranch(int headNode) {
-    final List<Integer> nodeIndexes = new ArrayList<>();
-
-    LOG.assertTrue(!myDoneNodes.get(headNode));
     myDoneNodes.set(headNode, true);
+    List<Integer> nodeIndexes = new ArrayList<>();
     nodeIndexes.add(headNode);
 
     final int startLayout = myGraphLayout.getLayoutIndex(headNode);
diff --git a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/GraphLayoutBuilder.kt b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/GraphLayoutBuilder.kt
index 2418b0428edb..08a7e25afc20 100644
--- a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/GraphLayoutBuilder.kt
+++ b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/GraphLayoutBuilder.kt
@@ -16,35 +16,47 @@ object GraphLayoutBuilder {
 
   @JvmStatic
   fun build(graph: LinearGraph, comparator: IntComparator): GraphLayoutImpl {
-    val heads = getSortedHeads(graph, comparator)
-
-    val layoutIndex = IntArray(graph.nodesCount())
-    val startLayoutIndexForHead = IntArray(heads.size)
-    var currentLayoutIndex = 1
-    for (i in heads.indices) {
-      startLayoutIndexForHead[i] = currentLayoutIndex
-      currentLayoutIndex = dfs(graph, heads.getInt(i), currentLayoutIndex, layoutIndex)
-    }
-    return GraphLayoutImpl(layoutIndex, heads, startLayoutIndexForHead)
+    return build(graph, emptySet(), comparator)
   }
 
-  private fun getSortedHeads(graph: LinearGraph, comparator: IntComparator): IntList {
-    val heads: IntList = IntArrayList()
-    for (i in 0 until graph.nodesCount()) {
-      if (LinearGraphUtils.getUpNodes(graph, i).isEmpty()) {
-        heads.add(i)
-      }
+  @JvmStatic
+  fun build(graph: LinearGraph, branches: Set<Int>, comparator: IntComparator): GraphLayoutImpl {
+    val allHeads = branches + graph.getHeads()
+    val sortedHeads = IntArrayList(allHeads).sortCatching(comparator)
+
+    val layoutIndex = IntArray(graph.nodesCount())
+    val startLayoutIndexForHead = IntArray(sortedHeads.size)
+    var currentLayoutIndex = 1
+    for (i in sortedHeads.indices) {
+      startLayoutIndexForHead[i] = currentLayoutIndex
+      currentLayoutIndex = dfs(graph, sortedHeads.getInt(i), currentLayoutIndex, layoutIndex)
     }
+    return GraphLayoutImpl(layoutIndex, sortedHeads, startLayoutIndexForHead)
+  }
+
+  /**
+   * Performs sorting, while catching exceptions from the comparator.
+   */
+  private fun IntList.sortCatching(comparator: IntComparator): IntList {
     try {
-      heads.sort(comparator)
+      sort(comparator)
     }
     catch (pce: ProcessCanceledException) {
       throw pce
     }
     catch (e: Exception) {
-      // protection against possible comparator flaws
       LOG.error(e)
     }
+    return this
+  }
+
+  private fun LinearGraph.getHeads(): IntList {
+    val heads = IntArrayList()
+    for (i in 0 until nodesCount()) {
+      if (LinearGraphUtils.getUpNodes(this, i).isEmpty()) {
+        heads.add(i)
+      }
+    }
     return heads
   }
 
diff --git a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/PermanentCommitsInfoImpl.kt b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/PermanentCommitsInfoImpl.kt
index e864868d83df..40390f9a37ee 100644
--- a/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/PermanentCommitsInfoImpl.kt
+++ b/platform/vcs-log/graph/src/com/intellij/vcs/log/graph/impl/permanent/PermanentCommitsInfoImpl.kt
@@ -9,6 +9,7 @@ import com.intellij.vcs.log.graph.utils.impl.CompressedIntList
 import com.intellij.vcs.log.graph.utils.impl.IntTimestampGetter
 import it.unimi.dsi.fastutil.ints.Int2ObjectMap
 import it.unimi.dsi.fastutil.ints.IntOpenHashSet
+import it.unimi.dsi.fastutil.ints.IntSet
 import java.util.*
 
 class PermanentCommitsInfoImpl<CommitId : Any> private constructor(val timestampGetter: TimestampGetter,
@@ -50,6 +51,10 @@ class PermanentCommitsInfoImpl<CommitId : Any> private constructor(val timestamp
   }
 
   override fun convertToNodeIds(commitIds: Collection<CommitId>): Set<Int> {
+    return convertToNodeIds(commitIds, false)
+  }
+
+  internal fun convertToNodeIds(commitIds: Collection<CommitId>, skipNotLoadedCommits: Boolean): IntSet {
     val result = IntOpenHashSet()
     for (i in commitIdIndexes.indices) {
       val commitId = commitIdIndexes[i]
@@ -57,9 +62,11 @@ class PermanentCommitsInfoImpl<CommitId : Any> private constructor(val timestamp
         result.add(i)
       }
     }
-    for (entry in notLoadedCommits.int2ObjectEntrySet()) {
-      if (commitIds.contains(entry.value)) {
-        result.add(entry.intKey)
+    if (!skipNotLoadedCommits) {
+      for (entry in notLoadedCommits.int2ObjectEntrySet()) {
+        if (commitIds.contains(entry.value)) {
+          result.add(entry.intKey)
+        }
       }
     }
     return result
diff --git a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/CompressedRefs.java b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/CompressedRefs.java
index 7fd82c1f2f37..184662d99b37 100644
--- a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/CompressedRefs.java
+++ b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/CompressedRefs.java
@@ -106,4 +106,8 @@ public final class CompressedRefs {
     myTags.keySet().intStream().forEach(result::add);
     return result;
   }
+
+  @NotNull Int2ObjectMap<List<VcsRef>> getBranches() {
+    return myBranches;
+  }
 }
diff --git a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/RefsModel.kt b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/RefsModel.kt
index 9dcfb5cf5db5..092fd2d72a7f 100644
--- a/platform/vcs-log/impl/src/com/intellij/vcs/log/data/RefsModel.kt
+++ b/platform/vcs-log/impl/src/com/intellij/vcs/log/data/RefsModel.kt
@@ -10,6 +10,8 @@ import com.intellij.vcs.log.VcsLogRefs
 import com.intellij.vcs.log.VcsRef
 import it.unimi.dsi.fastutil.ints.Int2ObjectMap
 import it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap
+import it.unimi.dsi.fastutil.ints.IntOpenHashSet
+import java.util.function.IntConsumer
 import java.util.stream.Collectors
 import java.util.stream.Stream
 
@@ -65,7 +67,14 @@ class RefsModel(val allRefsByRoot: Map<VirtualFile, CompressedRefs>, private val
                providers: Map<VirtualFile, VcsLogProvider>): RefsModel {
       val refsModel = RefsModel(refs, storage, providers)
 
-      storage.getCommitIds(heads).forEach { (head, commitId) -> refsModel.updateCacheForHead(head, commitId.root) }
+      val remainingHeads = IntOpenHashSet(heads)
+      refs.forEach { (root, refsForRoot) ->
+        refsForRoot.branches.keys.forEach(IntConsumer { commit ->
+          refsModel.updateCacheForHead(commit, root)
+          remainingHeads.remove(commit)
+        })
+      }
+      storage.getCommitIds(remainingHeads).forEach { (head, commitId) -> refsModel.updateCacheForHead(head, commitId.root) }
 
       return refsModel
     }