diff --git a/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h b/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h
index 4e82879651c..23e5206df20 100644
--- a/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h
+++ b/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h
@@ -19,8 +19,7 @@
 #define itkSymmetricEigenAnalysis_h
 
 #include "itkMacro.h"
-#include "itk_eigen.h"
-#include ITK_EIGEN(Eigenvalues)
+#include <Eigen/Eigenvalues>
 #include <numeric>
 #include <vector>
 // For GetPointerToMatrixData
diff --git a/Modules/Registration/Montage/include/itkTileMontage.hxx b/Modules/Registration/Montage/include/itkTileMontage.hxx
index dce24ce2ff3..496851368d3 100644
--- a/Modules/Registration/Montage/include/itkTileMontage.hxx
+++ b/Modules/Registration/Montage/include/itkTileMontage.hxx
@@ -25,8 +25,7 @@
 #include "itkThreadPool.h"
 #include "itkConfigure.h" // for ITK_USE_FFTWF and ITK_USE_FFTWD
 
-#include "itk_eigen.h"
-#include ITK_EIGEN(Sparse)
+#include <Eigen/Sparse>
 
 #include <algorithm>
 #include <cassert>
diff --git a/Modules/ThirdParty/Eigen3/src/itk_eigen.h.in b/Modules/ThirdParty/Eigen3/src/itk_eigen.h.in
index e4044ab999a..9eb65f01ddc 100644
--- a/Modules/ThirdParty/Eigen3/src/itk_eigen.h.in
+++ b/Modules/ThirdParty/Eigen3/src/itk_eigen.h.in
@@ -19,7 +19,14 @@
 #ifndef itk_eigen_h
 #define itk_eigen_h
 
-/* Usage:
+/* Legacy include shim. New code should write `#include <Eigen/Eigenvalues>`
+ * (or any other Eigen header) directly.  The Eigen3::Eigen CMake target,
+ * which is automatically linked when a module declares ITKEigen3 as a
+ * dependency in itk-module.cmake, provides the include path and (for
+ * bundled Eigen) the EIGEN_MPL2_ONLY define and Eigen-specific Clang
+ * warning suppressions.
+ *
+ * Legacy usage:
  *  ITK_EIGEN(Eigenvalues)
  *  If using a Eigen3 header containing non MPL2 code
  *  It would generate errors when using internal Eigen, but not with system Eigen.
diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt b/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt
index b3658c338be..32dc6eb748e 100644
--- a/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt
+++ b/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt
@@ -955,14 +955,25 @@ if(ITK_USE_EIGEN_MPL2_ONLY)
   target_compile_definitions (eigen_internal INTERFACE "EIGEN_MPL2_ONLY")
 endif()
 
-# BUILD: go one directory before to localize the headers:
-#   #include <itkeigen/Eigen/x>
-# INSTALL: headers require pre-prend itkeigen/Eigen/X.
+# Resolve both #include <Eigen/x> (preferred, ITKv6 canonical syntax) and
+# #include <itkeigen/Eigen/x> (legacy ITK_EIGEN(x) macro expansion).
 target_include_directories (eigen_internal SYSTEM INTERFACE
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>
+  $<INSTALL_INTERFACE:${INCLUDE_INSTALL_DIR}/itkeigen>
   $<INSTALL_INTERFACE:${INCLUDE_INSTALL_DIR}>
   )
 
+# Eigen headers trip several Clang warnings that don't fire elsewhere in ITK.
+target_compile_options (eigen_internal INTERFACE
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-alloca>
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-used-but-marked-unused>
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-unused-template>
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-missing-noreturn>
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-zero-as-null-pointer-constant>
+  $<$<COMPILE_LANG_AND_ID:CXX,Clang,AppleClang>:-Wno-deprecated>
+  )
+
 # Export as title case Eigen
 set_target_properties (eigen_internal PROPERTIES EXPORT_NAME Eigen)
 install (TARGETS eigen_internal EXPORT ITKInternalEigen3Targets)