diff -u squashfs4.2/squashfs-tools/mksquashfs.c squashfs4.2_fix/squashfs-tools/mksquashfs.c
--- squashfs4.2/squashfs-tools/mksquashfs.c	2011-02-28 23:24:10.000000000 +0100
+++ squashfs4.2_fix/squashfs-tools/mksquashfs.c	2013-09-16 00:32:22.115362300 +0200
@@ -25,6 +25,11 @@
 #define FALSE 0
 #define TRUE 1
 
+#ifdef __CYGWIN__
+#include <sys/termios.h>
+#define FNM_EXTMATCH  (1 << 5)
+#endif
+
 #include <pwd.h>
 #include <grp.h>
 #include <time.h>
@@ -51,10 +56,12 @@
 #include <sys/wait.h>
 
 #ifndef linux
+#ifndef __CYGWIN__
 #define __BYTE_ORDER BYTE_ORDER
 #define __BIG_ENDIAN BIG_ENDIAN
 #define __LITTLE_ENDIAN LITTLE_ENDIAN
 #include <sys/sysctl.h>
+#endif /* __CYGWIN__ */
 #else
 #include <endian.h>
 #include <sys/sysinfo.h>
@@ -137,7 +144,7 @@
 int block_size = SQUASHFS_FILE_SIZE, block_log;
 unsigned int id_count = 0;
 int file_count = 0, sym_count = 0, dev_count = 0, dir_count = 0, fifo_count = 0,
-	sock_count = 0;
+	sock_count = 0, exec_count = 0;
 
 /* write position within data section */
 long long bytes = 0, total_bytes = 0;
@@ -1196,6 +1203,41 @@
 }
 
 
+#ifdef __CYGWIN__
+int is_file_executable(char *filename)
+{
+	char header_elf[] = {0x7F, 'E', 'L', 'F'};
+	char header_sh[] = {'#', '!'};
+	int ret = FALSE;
+
+	FILE* f = fopen(filename, "rb");
+	if (f == NULL)
+		return FALSE;
+
+	char* buf = malloc(4 * sizeof(char));
+	if (buf == NULL)
+	{
+		fclose(f);
+		return FALSE;
+	}
+
+	if (fread(buf, 1, 4, f) != 4)
+	{
+		fclose(f);
+		free(buf);
+		return FALSE;
+	}
+
+	fclose(f);
+
+	ret = (memcmp(buf, header_elf, 4) == 0 || memcmp(buf, header_sh, 2) == 0);
+
+	free(buf);
+	return ret;
+}
+#endif
+
+
 int create_inode(squashfs_inode *i_no, struct dir_info *dir_info,
 	struct dir_ent *dir_ent, int type, long long byte_size,
 	long long start_block, unsigned int offset, unsigned int *block_list,
@@ -1246,6 +1288,15 @@
 		break;
 	}
 			
+#ifdef __CYGWIN__
+	if(type == SQUASHFS_FILE_TYPE) {
+		if(is_file_executable(filename)) {
+			exec_count++;
+			buf->st_mode = buf->st_mode | S_IRWXU | S_IRGRP | S_IXUSR | S_IROTH | S_IXOTH;
+		}
+	}
+#endif
+	//printf("FILE=%s, MODE=0x%x, TYPE=%d\n", filename, buf->st_mode, type);
 	base->mode = SQUASHFS_MODE(buf->st_mode);
 	base->uid = get_uid((unsigned int) global_uid == -1 ?
 		buf->st_uid : global_uid);
@@ -4062,6 +4113,10 @@
 
 	signal(SIGUSR1, sigusr1_handler);
 
+#ifdef __CYGWIN__
+	processors = atoi(getenv("NUMBER_OF_PROCESSORS"));
+#else
+
 	if(processors == -1) {
 #ifndef linux
 		int mib[2];
@@ -4083,6 +4138,7 @@
 		processors = sysconf(_SC_NPROCESSORS_ONLN);
 #endif
 	}
+#endif /* __CYGWIN__ */
 
 	thread = malloc((2 + processors * 2) * sizeof(pthread_t));
 	if(thread == NULL)
@@ -5392,6 +5448,9 @@
 		printf("No duplicate files removed\n");
 	printf("Number of inodes %d\n", inode_count);
 	printf("Number of files %d\n", file_count);
+#ifdef __CYGWIN__
+	printf("Number of executables %d\n", exec_count);
+#endif
 	if(!no_fragments)
 		printf("Number of fragments %d\n", fragments);
 	printf("Number of symbolic links  %d\n", sym_count);
diff -u squashfs4.2/squashfs-tools/read_fs.c squashfs4.2_fix/squashfs-tools/read_fs.c
--- squashfs4.2/squashfs-tools/read_fs.c	2011-02-11 16:49:24.000000000 +0100
+++ squashfs4.2_fix/squashfs-tools/read_fs.c	2012-10-25 16:39:51.971062000 +0200
@@ -33,9 +33,11 @@
 #include <sys/mman.h>
 
 #ifndef linux
+#ifndef __CYGWIN__
 #define __BYTE_ORDER BYTE_ORDER
 #define __BIG_ENDIAN BIG_ENDIAN
 #define __LITTLE_ENDIAN LITTLE_ENDIAN
+#endif /* __CYGWIN__ */
 #else
 #include <endian.h>
 #endif
diff -u squashfs4.2/squashfs-tools/unsquashfs.c squashfs4.2_fix/squashfs-tools/unsquashfs.c
--- squashfs4.2/squashfs-tools/unsquashfs.c	2011-02-28 23:27:06.000000000 +0100
+++ squashfs4.2_fix/squashfs-tools/unsquashfs.c	2012-10-25 16:44:41.610628400 +0200
@@ -32,6 +32,11 @@
 #include <sys/sysinfo.h>
 #include <sys/types.h>
 
+#ifdef __CYGWIN__
+#include <sys/termios.h>
+#define FNM_EXTMATCH  (1 << 5)
+#endif
+
 struct cache *fragment_cache, *data_cache;
 struct queue *to_reader, *to_deflate, *to_writer, *from_writer;
 pthread_t *thread, *deflator_thread;
@@ -1809,6 +1814,10 @@
 		EXIT_UNSQUASH("Failed to set signal mask in intialise_threads"
 			"\n");
 
+#ifdef __CYGWIN__
+	    processors = atoi(getenv("NUMBER_OF_PROCESSORS"));
+#else /* __CYGWIN__ */
+
 	if(processors == -1) {
 #ifndef linux
 		int mib[2];
@@ -1830,6 +1839,7 @@
 		processors = sysconf(_SC_NPROCESSORS_ONLN);
 #endif
 	}
+#endif /* __CYGWIN__ */
 
 	thread = malloc((3 + processors) * sizeof(pthread_t));
 	if(thread == NULL)
diff -u squashfs4.2/squashfs-tools/unsquashfs.h squashfs4.2_fix/squashfs-tools/unsquashfs.h
--- squashfs4.2/squashfs-tools/unsquashfs.h	2011-02-11 16:49:24.000000000 +0100
+++ squashfs4.2_fix/squashfs-tools/unsquashfs.h	2012-10-25 16:41:40.678279700 +0200
@@ -46,9 +46,11 @@
 #include <sys/time.h>
 
 #ifndef linux
+#ifndef __CYGWIN__
 #define __BYTE_ORDER BYTE_ORDER
 #define __BIG_ENDIAN BIG_ENDIAN
 #define __LITTLE_ENDIAN LITTLE_ENDIAN
+#endif /* __CYGWIN__ */
 #else
 #include <endian.h>
 #endif