diff --git a/Makefile b/Makefile
index 540f16d6..4cc1f2eb 100644
--- a/Makefile
+++ b/Makefile
@@ -138,6 +138,11 @@ BITS=32
 ifeq (x86_64,$(shell uname -m))
 BITS=64
 endif
+
+ifeq (aarch64,$(shell uname -m))
+BITS=64
+endif
+
 # msys will always be 32 bit so look at the cpu arch instead.
 ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
 	ifeq (1,$(MINGW))
@@ -155,6 +160,11 @@ ifeq (64,$(BITS))
 endif
 SSE_FLAG=-msse2
 
+ifeq (aarch64,$(shell uname -m))
+	BITS_FLAG =
+	SSE_FLAG =
+endif
+
 DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
 RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
diff --git a/aligner_sw.h b/aligner_sw.h
index add5c87d..e6a5cc71 100644
--- a/aligner_sw.h
+++ b/aligner_sw.h
@@ -70,7 +70,13 @@
 #include <iostream>
 #include <limits>
 #include "threading.h"
+
+#ifdef __aarch64__
+#include "SSE2NEON.h"
+#else
 #include <emmintrin.h>
+#endif
+
 #include "aligner_sw_common.h"
 #include "aligner_sw_nuc.h"
 #include "ds.h"
diff --git a/sse_util.h b/sse_util.h
index b5781f1a..45645718 100644
--- a/sse_util.h
+++ b/sse_util.h
@@ -24,7 +24,13 @@
 #include "ds.h"
 #include "limit.h"
 #include <iostream>
+
+#ifdef __aarch64__
+#include "SSE2NEON.h"
+#else
 #include <emmintrin.h>
+#endif
+
 
 class EList_m128i {
 public: