diff --git a/.gitignore b/.gitignore
index 9c2ec17..49f9f4b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,7 @@
 *.o
-fastahack
\ No newline at end of file
+fastahack
+libfastahack.a
+CMakeFiles
+CMakeCache.txt
+cmake_install.cmake
+Makefile
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..e556379
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 2.8)
+
+add_library(fastahack
+	FastaHack.cpp
+	Fasta.cpp
+	split.cpp
+	disorder.c
+)
+
+add_executable(fastahack-bin
+	FastaHack.cpp
+	disorder.c
+)
+
+set_target_properties(fastahack-bin
+	PROPERTIES OUTPUT_NAME fastahack
+)
+
+target_link_libraries(fastahack-bin
+	fastahack
+)
diff --git a/FastaHack.cpp b/FastaHack.cpp
index fac0963..b542abc 100644
--- a/FastaHack.cpp
+++ b/FastaHack.cpp
@@ -1,7 +1,9 @@
 #include "Fasta.h"
 #include <stdlib.h>
 #include <getopt.h>
+extern "C" {
 #include "disorder.h"
+}
 
 void printSummary() {
     cerr << "usage: fastahack [options] <fasta reference>" << endl
diff --git a/Makefile b/Makefile
deleted file mode 100644
index b0d847e..0000000
--- a/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-CXX=g++
-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64
-
-fastahack: Fasta.o FastaHack.cpp split.o disorder.o
-	$(CXX) $(CFLAGS) Fasta.o FastaHack.cpp split.o disorder.o -o fastahack
-
-Fasta.o: Fasta.h Fasta.cpp
-	$(CXX) $(CFLAGS) -c Fasta.cpp
-
-split.o: split.h split.cpp
-	$(CXX) $(CFLAGS) -c split.cpp
-
-disorder.o: disorder.c disorder.h
-	$(CXX) $(CFLAGS) -c disorder.c
-
-clean:
-	rm -f fastahack *.o
-
-.PHONY: clean
diff --git a/README b/README
index 5ccba37..7d82aa5 100644
--- a/README
+++ b/README
@@ -25,6 +25,15 @@ extraction without RAM-intensive file loading operations.  This makes fastahack
 a useful tool for bioinformaticists who need to quickly extract many
 subsequences from a reference FASTA sequence.
 
+Build:
+
+Cmake is required to build this project. Issue the following commands from the
+fastahack director:
+
+	% cmake .
+	% make
+	
+
 
 Notes: