diff --git a/gatb-core/thirdparty/hdf5/src/H5Odeprec.c b/gatb-core/thirdparty/hdf5/src/H5Odeprec.c
index 33ed78744..0c924789a 100644
--- a/gatb-core/thirdparty/hdf5/src/H5Odeprec.c
+++ b/gatb-core/thirdparty/hdf5/src/H5Odeprec.c
@@ -32,6 +32,7 @@
 /* Headers */
 /***********/
 #include "H5private.h"      /* Generic Functions    */
+#include "H5CXprivate.h"        /* API Contexts                             */
 #include "H5Eprivate.h"     /* Error handling       */
 #include "H5Opkg.h"         /* Object headers       */
 
diff --git a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp
index 5a2656610..881eada1f 100644
--- a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp
+++ b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp
@@ -10,6 +10,7 @@
  *
  */
 
+#include <cstdint>
 #include <fstream>
 #include <unordered_map>
 #include <map>
diff --git a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in
index a4c5e14d1..a0b2b51b5 100644
--- a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in
+++ b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in
@@ -10,6 +10,7 @@
  *
  */
 
+#include <cstdint>
 #include <fstream>
 #include <unordered_map>
 #include <map>