diff --git a/configure.ac b/configure.ac
index b05739f50a..ecdc00ab21 100644
--- a/configure.ac
+++ b/configure.ac
@@ -94,12 +94,19 @@ AC_INIT(configure.ac)
     # Checks for libraries.
 
     # Checks for header files.
-    AC_CHECK_HEADERS([arpa/inet.h inttypes.h limits.h netdb.h poll.h signal.h stdint.h stdlib.h string.h syslog.h sys/ioctl.h sys/prctl.h sys/socket.h sys/syscall.h netinet/in.h sys/time.h unistd.h windows.h winsock2.h ws2tcpip.h sched.h assert.h])
-    AC_CHECK_HEADERS([sys/socket.h net/if.h sys/mman.h], [], [],
+    AC_CHECK_HEADERS([arpa/inet.h assert.h ctype.h errno.h fcntl.h inttypes.h])
+    AC_CHECK_HEADERS([getopt.h])
+    AC_CHECK_HEADERS([limits.h netdb.h netinet/in.h poll.h sched.h signal.h])
+    AC_CHECK_HEADERS([stdarg.h stdint.h stdio.h stdlib.h string.h sys/ioctl.h])
+    AC_CHECK_HEADERS([syslog.h sys/prctl.h sys/socket.h sys/stat.h sys/syscall.h])
+    AC_CHECK_HEADERS([sys/time.h time.h unistd.h windows.h winsock2.h ws2tcpip.h])
+    AC_CHECK_HEADERS([sys/ioctl.h linux/if_ether.h linux/if_packet.h linux/filter.h])
+
+    AC_CHECK_HEADERS([sys/socket.h net/if.h sys/mman.h linux/if_arp.h], [], [],
     [[#ifdef HAVE_SYS_SOCKET_H
-#include <sys/types.h>
-#include <sys/socket.h>
-#endif
+        #include <sys/types.h>
+        #include <sys/socket.h>
+        #endif
     ]])
 
 
@@ -846,7 +853,7 @@ AC_INIT(configure.ac)
     if test "$with_libpcap_libraries" != "no"; then
         LDFLAGS="${LDFLAGS}  -L${with_libpcap_libraries}"
     fi
-    AC_CHECK_HEADERS([pcap.h pcap/pcap.h])
+    AC_CHECK_HEADERS([pcap.h pcap/pcap.h pcap/bpf.h])
 
     LIBPCAP=""
     AC_CHECK_LIB(pcap, pcap_open_live,, LIBPCAP="no", [-lpthread])
diff --git a/src/app-layer-htp-body.c b/src/app-layer-htp-body.c
index 970fc79faf..3795d1cd20 100644
--- a/src/app-layer-htp-body.c
+++ b/src/app-layer-htp-body.c
@@ -50,7 +50,6 @@
 #include "app-layer-htp.h"
 #include "app-layer-htp-file.h"
 #include "util-time.h"
-#include <htp/htp.h>
 
 #include "util-unittest.h"
 #include "util-unittest-helper.h"
diff --git a/src/app-layer-htp-file.c b/src/app-layer-htp-file.c
index 80aa6a349c..b8d526dcbc 100644
--- a/src/app-layer-htp-file.c
+++ b/src/app-layer-htp-file.c
@@ -47,7 +47,6 @@
 #include "util-debug.h"
 #include "app-layer-htp.h"
 #include "util-time.h"
-#include <htp/htp.h>
 
 #include "util-unittest.h"
 #include "util-unittest-helper.h"
diff --git a/src/conf.c b/src/conf.c
index be06794861..4d3f5e0836 100644
--- a/src/conf.c
+++ b/src/conf.c
@@ -36,8 +36,6 @@
  *   stays approach?
  */
 
-#include <string.h>
-
 #include "suricata-common.h"
 #include "conf.h"
 #include "util-unittest.h"
diff --git a/src/detect-engine-payload.c b/src/detect-engine-payload.c
index b6b507cf55..7d7306973f 100644
--- a/src/detect-engine-payload.c
+++ b/src/detect-engine-payload.c
@@ -452,7 +452,6 @@ static int PayloadTestSig13(void)
         "content:\"aa\"; content:\"aa\"; distance:0; content:\"aa\"; distance:0; "
         "byte_test:1,>,200,0,relative; sid:1;)";
 
-#include <sys/time.h>
     struct timeval tv_start, tv_end, tv_diff;
 
     gettimeofday(&tv_start, NULL);
diff --git a/src/detect-engine-sigorder.c b/src/detect-engine-sigorder.c
index b4a20ac56f..6f01e4de77 100644
--- a/src/detect-engine-sigorder.c
+++ b/src/detect-engine-sigorder.c
@@ -23,11 +23,6 @@
  * Signature ordering part of the detection engine.
  */
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <pcre.h>
-
 #include "suricata-common.h"
 #include "detect.h"
 #include "detect-flowbits.h"
diff --git a/src/detect-http-client-body.c b/src/detect-http-client-body.c
index a73238b736..b5336ff11a 100644
--- a/src/detect-http-client-body.c
+++ b/src/detect-http-client-body.c
@@ -53,7 +53,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-client-body.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-cookie.c b/src/detect-http-cookie.c
index 0d1b9d99a2..5fb7b399d7 100644
--- a/src/detect-http-cookie.c
+++ b/src/detect-http-cookie.c
@@ -55,7 +55,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-cookie.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-header.c b/src/detect-http-header.c
index 1fe3c45c56..1990ccd2f8 100644
--- a/src/detect-http-header.c
+++ b/src/detect-http-header.c
@@ -54,7 +54,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-header.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-method.c b/src/detect-http-method.c
index c2968d9069..8666fbf34b 100644
--- a/src/detect-http-method.c
+++ b/src/detect-http-method.c
@@ -54,7 +54,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-method.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-raw-header.c b/src/detect-http-raw-header.c
index 8f5ad07f24..88c15a2eeb 100644
--- a/src/detect-http-raw-header.c
+++ b/src/detect-http-raw-header.c
@@ -54,7 +54,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-raw-header.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-raw-uri.c b/src/detect-http-raw-uri.c
index f2dc7a0168..4b541d1075 100644
--- a/src/detect-http-raw-uri.c
+++ b/src/detect-http-raw-uri.c
@@ -50,7 +50,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-raw-uri.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-server-body.c b/src/detect-http-server-body.c
index 3982426345..b0d3db4847 100644
--- a/src/detect-http-server-body.c
+++ b/src/detect-http-server-body.c
@@ -54,7 +54,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-server-body.h"
 #include "stream-tcp.h"
diff --git a/src/detect-http-stat-code.c b/src/detect-http-stat-code.c
index c0cca4e2ad..c973a6f5b9 100644
--- a/src/detect-http-stat-code.c
+++ b/src/detect-http-stat-code.c
@@ -56,7 +56,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-stat-code.h"
 #include "stream-tcp-private.h"
diff --git a/src/detect-http-stat-msg.c b/src/detect-http-stat-msg.c
index 824b86ef3f..405e9a86e9 100644
--- a/src/detect-http-stat-msg.c
+++ b/src/detect-http-stat-msg.c
@@ -56,7 +56,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-stat-msg.h"
 #include "stream-tcp-private.h"
diff --git a/src/detect-http-ua.c b/src/detect-http-ua.c
index 0d1050e9c0..fdaa0e6335 100644
--- a/src/detect-http-ua.c
+++ b/src/detect-http-ua.c
@@ -53,7 +53,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "stream-tcp.h"
 #include "detect-http-ua.h"
diff --git a/src/detect-http-uri.c b/src/detect-http-uri.c
index 78d4003a06..6297939777 100644
--- a/src/detect-http-uri.c
+++ b/src/detect-http-uri.c
@@ -50,7 +50,6 @@
 
 #include "app-layer.h"
 
-#include <htp/htp.h>
 #include "app-layer-htp.h"
 #include "detect-http-uri.h"
 #include "detect-uricontent.h"
diff --git a/src/detect-pcre.c b/src/detect-pcre.c
index 847ac0d14e..3e10f1b258 100644
--- a/src/detect-pcre.c
+++ b/src/detect-pcre.c
@@ -57,7 +57,6 @@
 #include "app-layer-parser.h"
 #include "app-layer-htp.h"
 
-#include <htp/htp.h>
 #include "stream.h"
 
 
diff --git a/src/log-httplog.c b/src/log-httplog.c
index 4a83f57b3a..f4c6b426c6 100644
--- a/src/log-httplog.c
+++ b/src/log-httplog.c
@@ -24,8 +24,6 @@
  * Implements http logging portion of the engine.
  */
 
-#include <htp/dslib.h>
-
 #include "suricata-common.h"
 #include "debug.h"
 #include "detect.h"
diff --git a/src/source-af-packet.c b/src/source-af-packet.c
index 2591ea20c9..6848a333e9 100644
--- a/src/source-af-packet.c
+++ b/src/source-af-packet.c
@@ -56,17 +56,32 @@
 #include "runmodes.h"
 
 #ifdef HAVE_AF_PACKET
+
+#if HAVE_SYS_IOCTL_H
 #include <sys/ioctl.h>
+#endif
+
+#if HAVE_LINUX_IF_ETHER_H
 #include <linux/if_ether.h>
+#endif
+
+#if HAVE_LINUX_IF_PACKET_H
 #include <linux/if_packet.h>
+#endif
+
+#if HAVE_LINUX_IF_ARP_H
 #include <linux/if_arp.h>
+#endif
 
-#include <pcap/pcap.h>
-#include <pcap/bpf.h>
+#if HAVE_LINUX_FILTER_H
 #include <linux/filter.h>
 #endif
 
+#if HAVE_SYS_MMAN_H
 #include <sys/mman.h>
+#endif
+
+#endif /* HAVE_AF_PACKET */
 
 extern uint8_t suricata_ctl_flags;
 extern int max_pending_packets;
diff --git a/src/source-nfq.c b/src/source-nfq.c
index 03f48fa502..3d1626ac95 100644
--- a/src/source-nfq.c
+++ b/src/source-nfq.c
@@ -102,7 +102,6 @@ TmEcode NoNFQSupportExit(ThreadVars *tv, void *initdata, void **data)
 }
 
 #else /* implied we do have NFQ support */
-#include <pthread.h>
 
 extern int max_pending_packets;
 
diff --git a/src/suricata-common.h b/src/suricata-common.h
index 68e16e45c2..20d10a6014 100644
--- a/src/suricata-common.h
+++ b/src/suricata-common.h
@@ -40,22 +40,53 @@
 #include <config.h>
 #endif
 
+#if HAVE_STDIO_H
 #include <stdio.h>
+#endif
+
+#if HAVE_STDINT_h
 #include <stdint.h>
+#endif
+
+#if HAVE_STDARG_H
 #include <stdarg.h>
+#endif
+
+#ifdef HAVE_STDLIB_H
 #include <stdlib.h>
+#endif
+
+#if HAVE_ERRNO_H
 #include <errno.h>
+#endif
+
 #if HAVE_UNISTD_H
 #include <unistd.h>
 #endif
+
 #if HAVE_INTTYPES_H
 #include <inttypes.h>
 #endif
+
+#if HAVE_LIMITS_H
 #include <limits.h>
+#endif
+
+#if HAVE_CTYPE_H
 #include <ctype.h>
+#endif
+
+#if HAVE_STRING_H
 #include <string.h>
+#endif
+
+#if HAVE_FCNTL_H
 #include <fcntl.h>
+#endif
+
+#ifdef HAVE_TIME_H
 #include <time.h>
+#endif
 
 #if HAVE_SYS_SYSCALL_H
 #include <sys/syscall.h>
@@ -112,7 +143,9 @@
 #include <sys/socket.h>
 #endif
 
+#if HAVE_SYS_STAT_H
 #include <sys/stat.h>
+#endif
 
 #if HAVE_NETINET_IN_H
 #include <netinet/in.h>
@@ -156,6 +189,10 @@
 #include <pcap/pcap.h>
 #endif
 
+#ifdef HAVE_PCAP_BPF_H
+#include <pcap/bpf.h>
+#endif
+
 /* we need this to stringify the defines which are supplied at compiletime see:
    http://gcc.gnu.org/onlinedocs/gcc-3.4.1/cpp/Stringification.html#Stringification */
 #define xstr(s) str(s)
diff --git a/src/suricata.c b/src/suricata.c
index 27399279c1..1e5e2af97e 100644
--- a/src/suricata.c
+++ b/src/suricata.c
@@ -24,9 +24,13 @@
 #include "suricata-common.h"
 #include "config.h"
 
+#if HAVE_GETOPT_H
 #include <getopt.h>
+#endif
+
+#if HAVE_SIGNAL_H
 #include <signal.h>
-#include <pthread.h>
+#endif
 
 #ifdef HAVE_NSS
 #include <prinit.h>
diff --git a/src/tm-threads.c b/src/tm-threads.c
index 6a403752e6..883e9c3f1a 100644
--- a/src/tm-threads.c
+++ b/src/tm-threads.c
@@ -36,8 +36,6 @@
 #include "tmqh-packetpool.h"
 #include "threads.h"
 #include "util-debug.h"
-#include <pthread.h>
-#include <unistd.h>
 #include "util-privs.h"
 #include "util-cpu.h"
 #include "util-optimize.h"
diff --git a/src/util-cpu.c b/src/util-cpu.c
index f36b54702d..18cc12151f 100644
--- a/src/util-cpu.c
+++ b/src/util-cpu.c
@@ -23,11 +23,6 @@
  * Retrieve CPU information (configured CPUs, online CPUs)
  */
 
-#include <unistd.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
 #include "util-error.h"
 #include "util-debug.h"
 #include "suricata-common.h"
diff --git a/src/util-debug-filters.c b/src/util-debug-filters.c
index 72288d1623..6a8b9233de 100644
--- a/src/util-debug-filters.c
+++ b/src/util-debug-filters.c
@@ -24,17 +24,6 @@
  */
 
 #include "suricata-common.h"
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-
-#include "threads.h"
-#include "util-debug.h"
-#include "util-debug-filters.h"
-#include "util-error.h"
-#include "util-enum.h"
-#include <pthread.h>
 
 /* both of these are defined in util-debug.c */
 extern int sc_log_module_initialized;
diff --git a/src/util-decode-der-get.c b/src/util-decode-der-get.c
index 75972acbcc..f2ac3f74be 100644
--- a/src/util-decode-der-get.c
+++ b/src/util-decode-der-get.c
@@ -32,17 +32,6 @@
  *
  */
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-
-#include <inttypes.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <fcntl.h>
-
 #include "suricata-common.h"
 
 #include "util-decode-der.h"
diff --git a/src/util-decode-der.c b/src/util-decode-der.c
index 67ba9f2905..bc4eb7a706 100644
--- a/src/util-decode-der.c
+++ b/src/util-decode-der.c
@@ -43,17 +43,6 @@
  *
  */
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-
-#include <inttypes.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <fcntl.h>
-
 #include "suricata-common.h"
 
 #include "util-decode-der.h"