diff --git a/gtsam/inference/BayesNet-inl.h b/gtsam/inference/BayesNet-inl.h
index 5375b209f..903826e3a 100644
--- a/gtsam/inference/BayesNet-inl.h
+++ b/gtsam/inference/BayesNet-inl.h
@@ -117,18 +117,6 @@ namespace gtsam {
     }
   }
 
-  /* ************************************************************************* */
-  //template<class CONDITIONAL>
-  //bool BayesNet<CONDITIONAL>::permuteSeparatorWithInverse(
-  //    const Permutation& inversePermutation) {
-  //  bool separatorChanged = false;
-  //  BOOST_FOREACH(sharedConditional conditional, conditionals_) {
-  //    if (conditional->permuteSeparatorWithInverse(inversePermutation))
-  //      separatorChanged = true;
-  //  }
-  //  return separatorChanged;
-  //}
-
   /* ************************************************************************* */
   template<class CONDITIONAL>
   void BayesNet<CONDITIONAL>::push_back(const BayesNet<CONDITIONAL>& bn) {
diff --git a/gtsam/inference/BayesNet.h b/gtsam/inference/BayesNet.h
index f8aaa7d17..d3998656a 100644
--- a/gtsam/inference/BayesNet.h
+++ b/gtsam/inference/BayesNet.h
@@ -220,13 +220,6 @@ public:
   /** Permute the variables in the BayesNet */
   void permuteWithInverse(const Permutation& inversePermutation);
 
-  /**
-   * Permute the variables when only separator variables need to be permuted.
-   * Returns true if any reordered variables appeared in the separator and
-   * false if not.
-   */
-  //bool permuteSeparatorWithInverse(const Permutation& inversePermutation);
-
   iterator begin()          {return conditionals_.begin();}    ///<TODO: comment
   iterator end()            {return conditionals_.end();}      ///<TODO: comment
   reverse_iterator rbegin() {return conditionals_.rbegin();}  ///<TODO: comment
diff --git a/gtsam/inference/BayesTreeCliqueBase-inl.h b/gtsam/inference/BayesTreeCliqueBase-inl.h
index e682d5acf..5f01aa395 100644
--- a/gtsam/inference/BayesTreeCliqueBase-inl.h
+++ b/gtsam/inference/BayesTreeCliqueBase-inl.h
@@ -132,29 +132,6 @@ namespace gtsam {
     assertInvariants();
   }
 
-  /* ************************************************************************* */
-//  template<class DERIVED, class CONDITIONAL>
-//  bool BayesTreeCliqueBase<DERIVED, CONDITIONAL>::permuteSeparatorWithInverse(
-//      const Permutation& inversePermutation) {
-//    bool changed = conditional_->permuteSeparatorWithInverse(
-//        inversePermutation);
-//#ifndef NDEBUG
-//    if(!changed) {
-//      BOOST_FOREACH(Index& separatorKey, conditional_->parents()) {assert(separatorKey == inversePermutation[separatorKey]);}
-//      BOOST_FOREACH(const derived_ptr& child, children_) {
-//        assert(child->permuteSeparatorWithInverse(inversePermutation) == false);
-//      }
-//    }
-//#endif
-//    if (changed) {
-//      BOOST_FOREACH(const derived_ptr& child, children_) {
-//        (void) child->permuteSeparatorWithInverse(inversePermutation);
-//      }
-//    }
-//    assertInvariants();
-//    return changed;
-//  }
-
   /* ************************************************************************* */
   template<class DERIVED, class CONDITIONAL>
   bool BayesTreeCliqueBase<DERIVED, CONDITIONAL>::reduceSeparatorWithInverse(
diff --git a/gtsam/inference/BayesTreeCliqueBase.h b/gtsam/inference/BayesTreeCliqueBase.h
index a00980983..3a9a1ef78 100644
--- a/gtsam/inference/BayesTreeCliqueBase.h
+++ b/gtsam/inference/BayesTreeCliqueBase.h
@@ -178,13 +178,6 @@ namespace gtsam {
     /** Permute the variables in the whole subtree rooted at this clique */
     void permuteWithInverse(const Permutation& inversePermutation);
 
-    /** Permute variables when they only appear in the separators.  In this
-     * case the running intersection property will be used to prevent always
-     * traversing the whole tree.  Returns whether any separator variables in
-     * this subtree were reordered.
-     */
-    //bool permuteSeparatorWithInverse(const Permutation& inversePermutation);
-
     /** Permute variables when they only appear in the separators.  In this
      * case the running intersection property will be used to prevent always
      * traversing the whole tree.  Returns whether any separator variables in
diff --git a/gtsam/inference/IndexConditional.cpp b/gtsam/inference/IndexConditional.cpp
index 1a5e6d516..4167e56f2 100644
--- a/gtsam/inference/IndexConditional.cpp
+++ b/gtsam/inference/IndexConditional.cpp
@@ -43,23 +43,6 @@ namespace gtsam {
 #endif
   }
 
-  /* ************************************************************************* */
-  //bool IndexConditional::permuteSeparatorWithInverse(const Permutation& inversePermutation) {
-  //#ifndef NDEBUG
-  //  BOOST_FOREACH(KeyType key, frontals()) { assert(key == inversePermutation[key]); }
-  //#endif
-  //  bool parentChanged = false;
-  //  BOOST_FOREACH(KeyType& parent, parents()) {
-  //    KeyType newParent = inversePermutation[parent];
-  //    if(parent != newParent) {
-  //      parentChanged = true;
-  //      parent = newParent;
-  //    }
-  //  }
-  //  assertInvariants();
-  //  return parentChanged;
-  //}
-
   /* ************************************************************************* */
   bool IndexConditional::reduceSeparatorWithInverse(const internal::Reduction& inverseReduction) {
 #ifndef NDEBUG