diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 22694f2..0000000
--- a/src/Makefile
+++ /dev/null
@@ -1,86 +0,0 @@
-#
-#	Scyther Makefile
-#
-
-#
-#	DEBUG or optimization settings: uncomment a single line:
-#
-CFLAGS = -g3 -D DEBUG		# default usage, for e.g. with valgrind
-#CFLAGS = -g3 -D DEBUG -pg	# for code profiling with gprof
-#CFLAGS = -O3 -static -finline-functions -fomit-frame-pointer
-
-#
-#	Compiler and linkage
-#
-CC = gcc
-# Note that these paths must include the path to the argtable library.
-CPPFLAGS = -I/scratch/ccremers/include -I/usr/local/include -Wall
-LDFLAGS = -L/scratch/ccremers/lib -L/usr/local/lib
-LOADLIBS = -lfl
-LDLIBS = -largtable2
-OPTIONS = ${CPPFLAGS} ${CFLAGS} ${LDFLAGS}
-
-#
-#	Module set for the modelchecker
-#
-MODULES=memory.o terms.o termlists.o symbols.o knowledge.o runs.o modelchecker.o \
-report.o debug.o  mgu.o substitutions.o \
-match_basic.o \
-match_clp.o constraints.o \
-output.o latex.o \
-varbuf.o tracebuf.o attackminimize.o \
-tac.o parser.o compiler.o 
-
-#
-#	Dependencies
-#
-MODELCHECKER = ${MODULES} main.o
-
-all:		scyther tags
-
-${Target}.o:	${Target}.c
-		$(CC) $(OPTIONS) ${Target}.c -c
-
-scanner.c:	scanner.lex
-		flex scanner.lex
-		cp lex.yy.c scanner.c
-
-tok.h:		parser.c
-
-parser.c:	parser.y
-		bison -d -v parser.y
-		cp parser.tab.c parser.c
-		cmp -s parser.tab.h tok.h || cp parser.tab.h tok.h
-
-tags:		*.c *.h
-		ctags *.c *.h
-
-modules:	$(MODULES)
-
-scyther:	scanner.o $(MODELCHECKER)
-		$(CC) $(OPTIONS) $(MODELCHECKER) -o scyther $(LOADLIBS) $(LDLIBS)
-
-ptestmain.o scanner.o	: tok.h
-
-#
-#	Cleanup
-#
-clean:
-		rm -f *.o
-		rm -f scyther
-		rm -f scanner.c
-		rm -f parser.c
-		rm -f tok.h
-#
-#	Clean and rebuild: 'make new'
-#
-new:
-		make clean
-		make all
-
-#
-#	Make doxygen reference manuals. (in ../refman)
-#
-refman:		doxyconfig
-		doxygen doxyconfig
-
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..914688e
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,17 @@
+CC = @CC@
+VERSION = @VERSION@
+AM_CFLAGS = @CFLAGS@
+
+bin_PROGRAMS = scyther
+scyther_SOURCES = main.c \
+		 memory.c terms.c termlists.c symbols.c \
+		 knowledge.c runs.c modelchecker.c \
+		 report.c debug.c mgu.c substitutions.c \
+		 match_basic.c match_clp.c constraints.c \
+		 output.c latex.c varbuf.c tracebuf.c \
+		 attackminimize.c tac.c \
+		 compiler.c \
+		 scanner.lex parser.y
+scyther_LDADD = @LEXLIB@
+
+
diff --git a/src/configure.in b/src/configure.in
new file mode 100644
index 0000000..ae17204
--- /dev/null
+++ b/src/configure.in
@@ -0,0 +1,20 @@
+AC_INIT(main.c)
+AM_INIT_AUTOMAKE(Scyther, 0.2)
+            
+dnl find and test the C compiler
+AC_PROG_CC
+AC_LANG_C
+        
+AC_PROG_MAKE_SET
+               
+AC_HEADER_STDC
+AC_CHECK_FUNC(atol,,AC_MSG_ERROR(oops! no atol ?!?))
+AC_CHECK_LIB(argtable2, arg_parse,,AC_MSG_ERROR(Scyther requires the argtable2 package))
+AC_PROG_YACC
+AC_PROG_LEX
+                  
+VERSION="0.0.1"
+AC_SUBST(VERSION)
+
+dnl read Makefile.in and write Makefile
+AC_OUTPUT(Makefile)