diff --git a/CMakeLists.txt b/CMakeLists.txt
index 38ee89760..dd626bde8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -196,8 +196,7 @@ endif()
 ### See:  http://eigen.tuxfamily.org/bz/show_bug.cgi?id=704 (Householder QR MKL selection)
 ###       http://eigen.tuxfamily.org/bz/show_bug.cgi?id=705 (Fix MKL LLT return code)
 ###       http://eigen.tuxfamily.org/bz/show_bug.cgi?id=716 (Improved comma initialization)
-# option(GTSAM_USE_SYSTEM_EIGEN "Find and use system-installed Eigen. If 'off', use the one bundled with GTSAM" OFF)
-set(GTSAM_USE_SYSTEM_EIGEN OFF)
+option(GTSAM_USE_SYSTEM_EIGEN "Find and use system-installed Eigen. If 'off', use the one bundled with GTSAM" OFF)
 
 # Switch for using system Eigen or GTSAM-bundled Eigen
 if(GTSAM_USE_SYSTEM_EIGEN)
@@ -206,14 +205,22 @@ if(GTSAM_USE_SYSTEM_EIGEN)
 
 	find_package(Eigen3 REQUIRED)
 	include_directories(AFTER "${EIGEN3_INCLUDE_DIR}")
+	
+	# check if MKL is also enabled - can have one or the other, but not both!
+	if(EIGEN_USE_MKL_ALL)
+	  message(FATAL_ERROR "MKL cannot be used together with system-installed Eigen, as MKL support relies on patches which are not yet in the system-installed Eigen. Disable either GTSAM_USE_SYSTEM_EIGEN or GTSAM_WITH_EIGEN_MKL")
+	endif()
 else()
-	# Use bundled Eigen include paths e.g. <gtsam/3rdparty/Eigen/Eigen/Core>
+	# Use bundled Eigen include path. 
 	set(GTSAM_EIGEN_INCLUDE_PREFIX "gtsam/3rdparty/Eigen/")
 
 	# Clear any variables set by FindEigen3
 	if(EIGEN3_INCLUDE_DIR)
 		set(EIGEN3_INCLUDE_DIR NOTFOUND CACHE STRING "" FORCE)
 	endif()
+	# Add the bundled version of eigen to the include path so that it can still be included
+	# with  #include <Eigen/Core>
+	include_directories(BEFORE ${GTSAM_EIGEN_INCLUDE_PREFIX})
 endif()
 
 # Write Eigen include file with the paths for either the system Eigen or the GTSAM-bundled Eigen
@@ -389,6 +396,11 @@ if(NOT MSVC AND NOT XCODE_VERSION)
     message(STATUS "  C compilation flags            : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${cmake_build_type_toupper}}")
     message(STATUS "  C++ compilation flags          : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${cmake_build_type_toupper}}")
 endif()
+if(GTSAM_USE_SYSTEM_EIGEN)
+    message(STATUS "  Use System Eigen               : Yes")
+else()
+    message(STATUS "  Use System Eigen               : No")
+endif()
 if(GTSAM_USE_TBB)
 	message(STATUS "  Use Intel TBB                  : Yes")
 elseif(TBB_FOUND)
diff --git a/gtsam/base/Matrix.cpp b/gtsam/base/Matrix.cpp
index 7fa0992ca..9e56dfb6c 100644
--- a/gtsam/base/Matrix.cpp
+++ b/gtsam/base/Matrix.cpp
@@ -20,8 +20,8 @@
 #include <gtsam/base/timing.h>
 #include <gtsam/base/Vector.h>
 #include <gtsam/base/FastList.h>
-#include <gtsam/3rdparty/Eigen/Eigen/SVD>  
-#include <gtsam/3rdparty/Eigen/Eigen/LU>
+#include <Eigen/SVD>
+#include <Eigen/LU>
 
 #include <boost/foreach.hpp>
 #include <boost/tuple/tuple.hpp>
@@ -706,6 +706,7 @@ std::string formatMatrixIndented(const std::string& label, const Matrix& matrix,
   return ss.str();
 }
 
+/* ************************************************************************* */
 void inplace_QR(Matrix& A){
   size_t rows = A.rows();
   size_t cols = A.cols();
@@ -716,7 +717,13 @@ void inplace_QR(Matrix& A){
   HCoeffsType hCoeffs(size);
   RowVectorType temp(cols);
 
+#ifdef GTSAM_USE_SYSTEM_EIGEN
+  // System-Eigen is used, and MKL is off
+  Eigen::internal::householder_qr_inplace_blocked<Matrix, HCoeffsType>(A, hCoeffs, 48, temp.data());
+#else
+  // Patched Eigen is used, and MKL is either on or off
   Eigen::internal::householder_qr_inplace_blocked<Matrix, HCoeffsType>::run(A, hCoeffs, 48, temp.data());
+#endif
 
   zeroBelowDiagonal(A);
 }
diff --git a/gtsam/base/Matrix.h b/gtsam/base/Matrix.h
index 27b7ec8f7..53b040b9a 100644
--- a/gtsam/base/Matrix.h
+++ b/gtsam/base/Matrix.h
@@ -23,9 +23,9 @@
 #pragma once
 #include <gtsam/base/Vector.h>
 #include <boost/math/special_functions/fpclassify.hpp>
-#include <gtsam/3rdparty/Eigen/Eigen/Core>
-#include <gtsam/3rdparty/Eigen/Eigen/Cholesky>
-#include <gtsam/3rdparty/Eigen/Eigen/LU>
+#include <Eigen/Core>
+#include <Eigen/Cholesky>
+#include <Eigen/LU>
 #include <boost/format.hpp>
 #include <boost/tuple/tuple.hpp>
 
diff --git a/gtsam/base/OptionalJacobian.h b/gtsam/base/OptionalJacobian.h
index 2ea9d672e..81bf265a3 100644
--- a/gtsam/base/OptionalJacobian.h
+++ b/gtsam/base/OptionalJacobian.h
@@ -19,7 +19,7 @@
 
 #pragma once
 
-#include <gtsam/3rdparty/Eigen/Eigen/Dense>
+#include <Eigen/Dense>
 
 #ifndef OPTIONALJACOBIAN_NOBOOST
 #include <boost/optional.hpp>
diff --git a/gtsam/base/Vector.h b/gtsam/base/Vector.h
index fc543acc3..0869abc16 100644
--- a/gtsam/base/Vector.h
+++ b/gtsam/base/Vector.h
@@ -26,7 +26,7 @@
 #endif
 
 #include <gtsam/global_includes.h>
-#include <gtsam/3rdparty/Eigen/Eigen/Core>
+#include <Eigen/Core>
 #include <iosfwd>
 #include <list>
 
diff --git a/gtsam/config.h.in b/gtsam/config.h.in
index 64136511d..8d406e21f 100644
--- a/gtsam/config.h.in
+++ b/gtsam/config.h.in
@@ -42,6 +42,9 @@
 // Whether we are using TBB (if TBB was found and GTSAM_WITH_TBB is enabled in CMake)
 #cmakedefine GTSAM_USE_TBB
 
+// Whether we are using system-Eigen or our own patched version
+#cmakedefine GTSAM_USE_SYSTEM_EIGEN
+
 // Whether Eigen will use MKL (if MKL was found and GTSAM_WITH_EIGEN_MKL is enabled in CMake)
 #cmakedefine GTSAM_USE_EIGEN_MKL
 #cmakedefine EIGEN_USE_MKL_ALL // This is also defined in gtsam_eigen_includes.h