diff --git a/src/fix_nh.h b/src/fix_nh.h
index 624b0c8bb4..f137ecbe55 100644
--- a/src/fix_nh.h
+++ b/src/fix_nh.h
@@ -14,7 +14,7 @@
 #ifndef LMP_FIX_NH_H
 #define LMP_FIX_NH_H
 
-#include "fix.h"
+#include "fix.h"                // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/main.cpp b/src/main.cpp
index 9fb084aaea..d705db4e5b 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -12,9 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "lammps.h"
-#include <mpi.h>
 #include "input.h"
 
+#include <mpi.h>
+#include <cstdlib>
+
 #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE)
 #include <fenv.h>
 #endif
diff --git a/src/min.h b/src/min.h
index b23c9b6670..1db196a55e 100644
--- a/src/min.h
+++ b/src/min.h
@@ -14,7 +14,7 @@
 #ifndef LMP_MIN_H
 #define LMP_MIN_H
 
-#include "pointers.h"
+#include "pointers.h"           // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/neigh_list.h b/src/neigh_list.h
index 501188a724..c26b008136 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -14,7 +14,7 @@
 #ifndef LMP_NEIGH_LIST_H
 #define LMP_NEIGH_LIST_H
 
-#include "pointers.h"
+#include "pointers.h"           // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index 5350e01117..8a2f7a3989 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -20,8 +20,6 @@
 #include "memory.h"
 #include "error.h"
 
-#include <cstdlib>
-
 using namespace LAMMPS_NS;
 
 #define MAXLINE 1024        // max line length in dump file
diff --git a/tools/msi2lmp/src/WriteDataFile.c b/tools/msi2lmp/src/WriteDataFile.c
index c03eba71c5..a6f1615809 100644
--- a/tools/msi2lmp/src/WriteDataFile.c
+++ b/tools/msi2lmp/src/WriteDataFile.c
@@ -3,7 +3,6 @@
 */
 
 #include "msi2lmp.h"
-#include "Forcefield.h"
 
 #include <stdlib.h>
 
diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c
index efc929639a..b5e9a96293 100644
--- a/tools/msi2lmp/src/msi2lmp.c
+++ b/tools/msi2lmp/src/msi2lmp.c
@@ -151,7 +151,6 @@
 
 #include <stdlib.h>
 #include <string.h>
-#include <ctype.h>
 
 /* global variables */
 
diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h
index c9b1984444..af7978d181 100644
--- a/tools/msi2lmp/src/msi2lmp.h
+++ b/tools/msi2lmp/src/msi2lmp.h
@@ -34,7 +34,7 @@
 * compatibility with the obsolete LAMMPS version written in Fortran 90.
 */
 
-# include <stdio.h>
+#include <stdio.h>              /* IWYU pragma: export */
 
 #define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018"