diff --git a/MANIFEST.in b/MANIFEST.in
index 58ab7850..540e65ac 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -14,11 +14,15 @@ include pysam/c*.c
 include pysam/*.c
 include pysam/*.h
 include samtools/configure
+include samtools/config.mk.in
+include samtools/config.h.in
 include samtools/*.h
 include samtools/*/*.h
 include htslib/*.c
 include htslib/*.h
 include htslib/configure
+include htslib/config.mk.in
+include htslib/config.h.in
 include htslib/htslib/*.h
 include htslib/cram/*.c
 include htslib/cram/*.h