diff --git a/CMakeLists.txt b/CMakeLists.txt
index 20e8cebffb23..8dd660d9fd7f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -214,10 +214,6 @@ drake_add_external(drake LOCAL PUBLIC CMAKE ALWAYS
   BINARY_DIR ${PROJECT_BINARY_DIR}/drake
   ${DRAKE_BUILD_COMMANDS}
   CMAKE_ARGS
-    -DJava_JAVA_EXECUTABLE=${Java_JAVA_EXECUTABLE}
-    -DJava_JAVAC_EXECUTABLE=${Java_JAVAC_EXECUTABLE}
-    -DJava_JAVAH_EXECUTABLE=${Java_JAVAH_EXECUTABLE}
-    -DJava_VERSION_STRING=${Java_VERSION_STRING}
     -DWITH_PYTHON_3=${WITH_PYTHON_3}
     -DDISABLE_MATLAB=${DISABLE_MATLAB}
   DEPENDS
diff --git a/cmake/DrakeExternals.cmake b/cmake/DrakeExternals.cmake
index 9427493442e2..370f115dd21e 100644
--- a/cmake/DrakeExternals.cmake
+++ b/cmake/DrakeExternals.cmake
@@ -119,6 +119,11 @@ macro(drake_add_cmake_external PROJECT)
       -DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
       -DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS}
       -DCMAKE_STATIC_LINKER_FLAGS:STRING=${CMAKE_STATIC_LINKER_FLAGS}
+      -DJava_JAVA_EXECUTABLE:FILEPATH=${Java_JAVA_EXECUTABLE}
+      -DJava_JAVAC_EXECUTABLE:FILEPATH=${Java_JAVAC_EXECUTABLE}
+      -DJava_JAVAH_EXECUTABLE:FILEPATH=${Java_JAVAH_EXECUTABLE}
+      -DJava_VERSION_STRING:STRING=${Java_VERSION_STRING}
+      -DCMAKE_JAVA_COMPILE_FLAGS:STRING=${CMAKE_JAVA_COMPILE_FLAGS}
       ${_ext_VERBOSE}
       ${_ext_CMAKE_ARGS})
 endmacro()
diff --git a/cmake/DrakePlatform.cmake b/cmake/DrakePlatform.cmake
index c8855e287957..5b6a2a3e5609 100644
--- a/cmake/DrakePlatform.cmake
+++ b/cmake/DrakePlatform.cmake
@@ -1,3 +1,51 @@
+#------------------------------------------------------------------------------
+function(drake_get_matlab_jvm_version)
+  # Find matlab
+  find_program(MATLAB_EXECUTABLE matlab)
+
+  if(MATLAB_EXECUTABLE AND NOT MATLAB_JVM_VERSION)
+    # Set arguments for running matlab
+    set(_args -nodesktop -nodisplay -nosplash)
+    if(WIN32)
+      set(_args ${_args} -wait)
+    endif()
+
+    # Ask matlab for its JVM version
+    execute_process(
+      COMMAND ${MATLAB_EXECUTABLE} ${_args} -r "version -java,quit"
+      RESULT_VARIABLE _result
+      ERROR_VARIABLE _output
+      OUTPUT_VARIABLE _output
+      TIMEOUT 180)
+
+    # Test for a valid result
+    if(NOT _result AND _output MATCHES "Java ([0-9]+\\.[0-9]+)\\.[0-9_.]+")
+      set(MATLAB_JVM_VERSION ${CMAKE_MATCH_1} CACHE INTERNAL "")
+      set(_jsdk_version "${Java_VERSION_MAJOR}.${Java_VERSION_MINOR}")
+
+      # Compare against JSDK version
+      if(NOT _matlab_jvm_version VERSION_EQUAL _jsdk_version)
+        message(WARNING
+        "MATLAB JVM version (${MATLAB_JVM_VERSION}) does not match "
+        "installed Java SDK version (${_jsdk_version})")
+
+        # If JSDK is newer, set build options to build Java code compatible
+        # with the matlab JVM
+        if(MATLAB_JVM_VERSION VERSION_LESS _jsdk_version)
+          set(CMAKE_JAVA_COMPILE_FLAGS
+            -source ${MATLAB_JVM_VERSION}
+            -target ${MATLAB_JVM_VERSION}
+            CACHE INTERNAL "")
+        endif()
+      endif()
+    else()
+      message(WARNING "Could not determine MATLAB JVM version")
+    endif()
+  endif()
+endfunction()
+
+###############################################################################
+
 # Check minimum compiler requirements
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
   message(FATAL_ERROR "GCC version must be at least 4.9")
@@ -16,9 +64,16 @@ if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 endif()
 message(STATUS CMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX})
 
-# Require Java at the super-build level since libbot cannot configure without finding Java
+# Require Java at the super-build level since libbot cannot configure without
+# finding Java
 find_package(Java 1.6 REQUIRED)
 include(UseJava)
 
+# If matlab is in use, try to determine its JVM version, as we need to build
+# all externals to the same version
+if(NOT DISABLE_MATLAB)
+  drake_get_matlab_jvm_version()
+endif()
+
 # Choose your python (major) version
 option(WITH_PYTHON_3 "Force Drake to use python 3 instead of python 2" OFF)
diff --git a/drake/CMakeLists.txt b/drake/CMakeLists.txt
index e2c2a9c2f9c3..c7fd6f4627fe 100644
--- a/drake/CMakeLists.txt
+++ b/drake/CMakeLists.txt
@@ -139,29 +139,6 @@ else()
   # along with what is needed to use matlab_add_unit_test
   if(MATLAB_FOUND)
     find_package(Matlab COMPONENTS MAIN_PROGRAM REQUIRED)
-
-    set(Matlab_Java_MAIN_PROGRAM_ARGS -nodesktop -nodisplay -nosplash)
-    if(WIN32)
-      set(Matlab_Java_MAIN_PROGRAM_ARGS ${Matlab_Java_MAIN_PROGRAM_ARGS} -wait)
-    endif()
-    execute_process(
-      COMMAND ${Matlab_MAIN_PROGRAM} ${Matlab_Java_MAIN_PROGRAM_ARGS} -r "version -java,quit"
-      RESULT_VARIABLE Matlab_Java_RESULT_VARIABLE
-      ERROR_VARIABLE Matlab_Java_OUTPUT_VARIABLE
-      OUTPUT_VARIABLE Matlab_Java_OUTPUT_VARIABLE
-      TIMEOUT 180)
-    if(NOT Matlab_Java_RESULT_VARIABLE AND Matlab_Java_OUTPUT_VARIABLE MATCHES "Java ([0-9]+\\.[0-9]+)\\.[0-9_.]+")
-      set(Matlab_Java_VERSION_MAJOR_MINOR ${CMAKE_MATCH_1})
-      set(Java_VERSION_MAJOR_MINOR "${Java_VERSION_MAJOR}.${Java_VERSION_MINOR}")
-      if(NOT Matlab_Java_VERSION_MAJOR_MINOR VERSION_EQUAL Java_VERSION_MAJOR_MINOR)
-        message(WARNING "MATLAB JVM version (${Matlab_Java_VERSION_MAJOR_MINOR}) does not match installed Java SDK version (${Java_VERSION_MAJOR_MINOR})")
-        if(Matlab_Java_VERSION_MAJOR_MINOR VERSION_LESS Java_VERSION_MAJOR_MINOR)
-          set(CMAKE_JAVA_COMPILE_FLAGS -source ${Matlab_Java_VERSION_MAJOR_MINOR} -target ${Matlab_Java_VERSION_MAJOR_MINOR})
-        endif()
-      endif()
-    else()
-      message(WARNING "Could not determine MATLAB JVM version")
-    endif()
   endif()
 endif()