diff --git a/.gitignore b/.gitignore
index 8ea5d75ab..f57939364 100644
--- a/.gitignore
+++ b/.gitignore
@@ -60,6 +60,7 @@ __pycache__/
 /External/catch/catch/
 /External/CoordGen/coordgen/
 /External/CoordGen/maeparser/
+/External/Eigen/eigen/
 /External/FreeSASA/freesasa-2.0.1/
 /External/INCHI-API/INCHI-1-SRC/
 /External/INCHI-API/src/
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fe97563c1..c04b1eb0a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -380,20 +380,18 @@ endif(RDK_BUILD_PYTHON_WRAPPERS)
 string(REGEX MATCH "clang" CMAKE_COMPILER_IS_CLANG "${CMAKE_C_COMPILER}")
 
 find_package(Eigen3)
-if(EIGEN3_FOUND)
+if(RDK_BUILD_DESCRIPTORS3D)
+  if(NOT EIGEN3_FOUND)
+    add_subdirectory(External/Eigen)
+  endif()
+  target_compile_definitions(rdkit_base INTERFACE "-DRDK_BUILD_DESCRIPTORS3D")
+endif()
+
+if(TARGET Eigen3::Eigen)
   target_compile_definitions(rdkit_base INTERFACE "-DRDK_HAS_EIGEN3")
   target_link_libraries(rdkit_base INTERFACE Eigen3::Eigen)
   set(RDK_HAS_EIGEN ON)
-endif(EIGEN3_FOUND)
-
-if(RDK_BUILD_DESCRIPTORS3D)
-  if(EIGEN3_FOUND)
-    target_compile_definitions(rdkit_base INTERFACE "-DRDK_BUILD_DESCRIPTORS3D")
-  else(EIGEN3_FOUND)
-    message("Eigen3 not found, some Mol descriptors will not be built.")
-    set(RDK_BUILD_DESCRIPTORS3D OFF)
-  endif(EIGEN3_FOUND)
-endif(RDK_BUILD_DESCRIPTORS3D)
+endif()
 
 if(RDK_BUILD_THREADSAFE_SSS)
   find_package (Threads)
diff --git a/External/Eigen/CMakeLists.txt b/External/Eigen/CMakeLists.txt
new file mode 100644
index 000000000..1ce512c89
--- /dev/null
+++ b/External/Eigen/CMakeLists.txt
@@ -0,0 +1,17 @@
+include(ExternalProject)
+set(EIGEN3_VERSION "3.3.9")
+set(EIGEN3_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/eigen)
+ExternalProject_Add(Eigen
+  GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+  GIT_TAG ${EIGEN3_VERSION}
+  GIT_SHALLOW ON
+  SOURCE_DIR ${EIGEN3_INCLUDE_DIR}
+  CONFIGURE_COMMAND ""
+  BUILD_COMMAND ""
+  INSTALL_COMMAND ""
+)
+
+add_library(Eigen3::Eigen INTERFACE IMPORTED GLOBAL)
+set_target_properties(Eigen3::Eigen PROPERTIES
+  INTERFACE_INCLUDE_DIRECTORIES ${EIGEN3_INCLUDE_DIR})
+add_dependencies(Eigen3::Eigen Eigen)