diff --git a/libraries/AP_HAL_Linux/AnalogIn_IIO.cpp b/libraries/AP_HAL_Linux/AnalogIn_IIO.cpp
index 7326046400..8d27d78a0f 100644
--- a/libraries/AP_HAL_Linux/AnalogIn_IIO.cpp
+++ b/libraries/AP_HAL_Linux/AnalogIn_IIO.cpp
@@ -35,7 +35,7 @@ void AnalogSource_IIO::init_pins(void)
         strncpy(buf, IIO_ANALOG_IN_DIR, sizeof(buf));
         strncat(buf, AnalogSource_IIO::analog_sources[i], sizeof(buf) - strlen(buf) - 1);
 
-        fd_analog_sources[i] = open(buf, O_RDONLY | O_NONBLOCK);
+        fd_analog_sources[i] = open(buf, O_RDONLY | O_NONBLOCK | O_CLOEXEC);
     }
 }
 
diff --git a/libraries/AP_HAL_Linux/AnalogIn_Navio2.cpp b/libraries/AP_HAL_Linux/AnalogIn_Navio2.cpp
index 789e852c06..44373f8f5d 100644
--- a/libraries/AP_HAL_Linux/AnalogIn_Navio2.cpp
+++ b/libraries/AP_HAL_Linux/AnalogIn_Navio2.cpp
@@ -27,7 +27,7 @@ void AnalogSource_Navio2::set_channel(uint8_t pin)
         ::close(_fd);
     }
 
-    _fd = ::open(channel_path, O_RDONLY);
+    _fd = ::open(channel_path, O_RDONLY|O_CLOEXEC);
 
     if (_fd < 0) {
         hal.console->printf("%s not opened: %s\n", channel_path, strerror(errno));
diff --git a/libraries/AP_HAL_Linux/CameraSensor.cpp b/libraries/AP_HAL_Linux/CameraSensor.cpp
index 568b0dfee8..63f45397a0 100644
--- a/libraries/AP_HAL_Linux/CameraSensor.cpp
+++ b/libraries/AP_HAL_Linux/CameraSensor.cpp
@@ -30,7 +30,7 @@ bool CameraSensor::set_format(uint32_t width, uint32_t height, uint32_t format)
     struct v4l2_subdev_format fmt;
     int ret, fd;
 
-    fd = open(_device_path, O_RDWR);
+    fd = open(_device_path, O_RDWR | O_CLOEXEC);
     if (fd < 0) {
         return false;
     }
diff --git a/libraries/AP_HAL_Linux/GPIO_BBB.cpp b/libraries/AP_HAL_Linux/GPIO_BBB.cpp
index 7936287665..b757b242bb 100644
--- a/libraries/AP_HAL_Linux/GPIO_BBB.cpp
+++ b/libraries/AP_HAL_Linux/GPIO_BBB.cpp
@@ -29,7 +29,7 @@ void GPIO_BBB::init()
     // Idea taken from https://groups.google.com/forum/#!msg/beagleboard/OYFp4EXawiI/Mq6s3sg14HoJ
 
     uint8_t bank_enable[3] = { 5, 65, 105 };
-    int export_fd = open("/sys/class/gpio/export", O_WRONLY);
+    int export_fd = open("/sys/class/gpio/export", O_WRONLY | O_CLOEXEC);
     if (export_fd == -1) {
         AP_HAL::panic("unable to open /sys/class/gpio/export");
     }
@@ -40,7 +40,7 @@ void GPIO_BBB::init()
 
 
     /* open /dev/mem */
-    if ((mem_fd = open("/dev/mem", O_RDWR|O_SYNC) ) < 0) {
+    if ((mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC)) < 0) {
             printf("can't open /dev/mem \n");
             exit (-1);
     }
diff --git a/libraries/AP_HAL_Linux/GPIO_RPI.cpp b/libraries/AP_HAL_Linux/GPIO_RPI.cpp
index 3e6cea1901..8937949b69 100644
--- a/libraries/AP_HAL_Linux/GPIO_RPI.cpp
+++ b/libraries/AP_HAL_Linux/GPIO_RPI.cpp
@@ -48,7 +48,7 @@ void GPIO_RPI::init()
     int rpi_version = UtilRPI::from(hal.util)->get_rpi_version();
     uint32_t gpio_address = rpi_version == 1 ? GPIO_BASE(BCM2708_PERI_BASE)   : GPIO_BASE(BCM2709_PERI_BASE);
 
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd < 0) {
         AP_HAL::panic("Can't open /dev/mem");
     }
diff --git a/libraries/AP_HAL_Linux/OpticalFlow_Onboard.cpp b/libraries/AP_HAL_Linux/OpticalFlow_Onboard.cpp
index a069a240d1..2137b64c3d 100644
--- a/libraries/AP_HAL_Linux/OpticalFlow_Onboard.cpp
+++ b/libraries/AP_HAL_Linux/OpticalFlow_Onboard.cpp
@@ -342,7 +342,7 @@ void OpticalFlow_Onboard::_run_optflow()
         gyro_rate.z = rate_z;
 
 #ifdef OPTICALFLOW_ONBOARD_RECORD_VIDEO
-        int fd = open(OPTICALFLOW_ONBOARD_VIDEO_FILE, O_CREAT | O_WRONLY
+        int fd = open(OPTICALFLOW_ONBOARD_VIDEO_FILE, O_CLOEXEC | O_CREAT | O_WRONLY
                 | O_APPEND, S_IRUSR | S_IWUSR | S_IRGRP |
                 S_IWGRP | S_IROTH | S_IWOTH);
 	    if (fd != -1) {
diff --git a/libraries/AP_HAL_Linux/RCInput_115200.cpp b/libraries/AP_HAL_Linux/RCInput_115200.cpp
index 47140996ae..7fb225023d 100644
--- a/libraries/AP_HAL_Linux/RCInput_115200.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_115200.cpp
@@ -37,7 +37,7 @@ using namespace Linux;
 
 void RCInput_115200::init()
 {
-    fd = open(device_path, O_RDWR | O_NONBLOCK);
+    fd = open(device_path, O_RDWR | O_NONBLOCK | O_CLOEXEC);
     if (fd != -1) {
         struct termios options;
 
diff --git a/libraries/AP_HAL_Linux/RCInput_AioPRU.cpp b/libraries/AP_HAL_Linux/RCInput_AioPRU.cpp
index c4ce642f10..69f4e3221f 100644
--- a/libraries/AP_HAL_Linux/RCInput_AioPRU.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_AioPRU.cpp
@@ -35,7 +35,7 @@ using namespace Linux;
 
 void RCInput_AioPRU::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }
diff --git a/libraries/AP_HAL_Linux/RCInput_Navio2.cpp b/libraries/AP_HAL_Linux/RCInput_Navio2.cpp
index c32adaf2f0..edd7eee78c 100644
--- a/libraries/AP_HAL_Linux/RCInput_Navio2.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_Navio2.cpp
@@ -65,7 +65,7 @@ int RCInput_Navio2::open_channel(int channel)
         AP_HAL::panic("[RCInput_Navio2]: not enough memory\n");
     }
 
-    int fd = ::open(channel_path, O_RDONLY);
+    int fd = ::open(channel_path, O_RDONLY|O_CLOEXEC);
 
     free(channel_path);
 
diff --git a/libraries/AP_HAL_Linux/RCInput_PRU.cpp b/libraries/AP_HAL_Linux/RCInput_PRU.cpp
index aa14cdeeb9..804072d9e5 100644
--- a/libraries/AP_HAL_Linux/RCInput_PRU.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_PRU.cpp
@@ -27,7 +27,7 @@ using namespace Linux;
 
 void RCInput_PRU::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }
diff --git a/libraries/AP_HAL_Linux/RCInput_RPI.cpp b/libraries/AP_HAL_Linux/RCInput_RPI.cpp
index 339c34d7d2..096c1ff2c5 100644
--- a/libraries/AP_HAL_Linux/RCInput_RPI.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_RPI.cpp
@@ -109,12 +109,12 @@ Memory_table::Memory_table(uint32_t page_count, int version)
     _phys_pages = (void**)malloc(page_count * sizeof(void*));
     _page_count = page_count;
  
-    if ((fdMem = open("/dev/mem", O_RDWR | O_SYNC)) < 0) {
+    if ((fdMem = open("/dev/mem", O_RDWR | O_SYNC | O_CLOEXEC)) < 0) {
         fprintf(stderr,"Failed to open /dev/mem\n");
         exit(-1);
     }
 
-    if ((file = open("/proc/self/pagemap", O_RDWR | O_SYNC)) < 0) {
+    if ((file = open("/proc/self/pagemap", O_RDWR | O_SYNC | O_CLOEXEC)) < 0) {
         fprintf(stderr,"Failed to open /proc/self/pagemap\n");
         exit(-1);
     }
@@ -216,7 +216,7 @@ void RCInput_RPI::set_physical_addresses(int version)
 //Map peripheral to virtual memory
 void* RCInput_RPI::map_peripheral(uint32_t base, uint32_t len)
 {
-    int fd = open("/dev/mem", O_RDWR);
+    int fd = open("/dev/mem", O_RDWR | O_CLOEXEC);
     void * vaddr;
 
     if (fd < 0) {
diff --git a/libraries/AP_HAL_Linux/RCInput_SBUS.cpp b/libraries/AP_HAL_Linux/RCInput_SBUS.cpp
index 312e3a1193..167ccd9310 100644
--- a/libraries/AP_HAL_Linux/RCInput_SBUS.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_SBUS.cpp
@@ -38,7 +38,7 @@ using namespace Linux;
 
 void RCInput_SBUS::init()
 {
-    fd = open(device_path, O_RDWR | O_NONBLOCK);
+    fd = open(device_path, O_RDWR | O_NONBLOCK | O_CLOEXEC);
     if (fd != -1) {
         printf("Opened SBUS input %s fd=%d\n", device_path, (int)fd);
         fflush(stdout);
@@ -107,7 +107,7 @@ void RCInput_SBUS::_timer_tick(void)
 #if SBUS_DEBUG_LOG
     static int logfd = -1;
     if (logfd == -1) {
-        logfd = open("sbus.log", O_WRONLY|O_CREAT|O_TRUNC, 0644);
+        logfd = open("sbus.log", O_WRONLY|O_CREAT|O_TRUNC|O_CLOEXEC, 0644);
     }
 #endif
 
diff --git a/libraries/AP_HAL_Linux/RCInput_UART.cpp b/libraries/AP_HAL_Linux/RCInput_UART.cpp
index 994aa6ff90..ae58c906e4 100644
--- a/libraries/AP_HAL_Linux/RCInput_UART.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_UART.cpp
@@ -17,7 +17,7 @@ using namespace Linux;
 
 RCInput_UART::RCInput_UART(const char *path)
 {
-    _fd = open(path, O_RDONLY|O_NOCTTY|O_NONBLOCK|O_NDELAY);
+    _fd = open(path, O_RDONLY|O_NOCTTY|O_NONBLOCK|O_NDELAY|O_CLOEXEC);
     if (_fd < 0) {
         AP_HAL::panic("RCInput_UART: Error opening '%s': %s",
                              path, strerror(errno));
diff --git a/libraries/AP_HAL_Linux/RCInput_ZYNQ.cpp b/libraries/AP_HAL_Linux/RCInput_ZYNQ.cpp
index 65e4f397bc..675235ba96 100644
--- a/libraries/AP_HAL_Linux/RCInput_ZYNQ.cpp
+++ b/libraries/AP_HAL_Linux/RCInput_ZYNQ.cpp
@@ -24,7 +24,7 @@ using namespace Linux;
 
 void RCInput_ZYNQ::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }
diff --git a/libraries/AP_HAL_Linux/RCOutput_AioPRU.cpp b/libraries/AP_HAL_Linux/RCOutput_AioPRU.cpp
index fdd6cff9a2..e77409481b 100644
--- a/libraries/AP_HAL_Linux/RCOutput_AioPRU.cpp
+++ b/libraries/AP_HAL_Linux/RCOutput_AioPRU.cpp
@@ -36,7 +36,7 @@ void RCOutput_AioPRU::init()
 
    signal(SIGBUS,catch_sigbus);
 
-   mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+   mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
 
    pwm = (struct pwm*) mmap(0, 0x1000, PROT_READ|PROT_WRITE, MAP_SHARED, mem_fd, RCOUT_PRUSS_RAM_BASE);
    iram = (uint32_t*)mmap(0, 0x2000, PROT_READ|PROT_WRITE, MAP_SHARED, mem_fd, RCOUT_PRUSS_IRAM_BASE);
diff --git a/libraries/AP_HAL_Linux/RCOutput_PRU.cpp b/libraries/AP_HAL_Linux/RCOutput_PRU.cpp
index 30f476a302..6e5f9c6b38 100644
--- a/libraries/AP_HAL_Linux/RCOutput_PRU.cpp
+++ b/libraries/AP_HAL_Linux/RCOutput_PRU.cpp
@@ -29,7 +29,7 @@ void RCOutput_PRU::init()
 {
     uint32_t mem_fd;
     signal(SIGBUS,catch_sigbus);
-    mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     sharedMem_cmd = (struct pwm_cmd *) mmap(0, 0x1000, PROT_READ|PROT_WRITE,
                                             MAP_SHARED, mem_fd, RCOUT_PRUSS_SHAREDRAM_BASE);
     close(mem_fd);
diff --git a/libraries/AP_HAL_Linux/RCOutput_ZYNQ.cpp b/libraries/AP_HAL_Linux/RCOutput_ZYNQ.cpp
index f68e7d3ee9..f67790f725 100644
--- a/libraries/AP_HAL_Linux/RCOutput_ZYNQ.cpp
+++ b/libraries/AP_HAL_Linux/RCOutput_ZYNQ.cpp
@@ -37,7 +37,7 @@ void RCOutput_ZYNQ::init()
 {
     uint32_t mem_fd;
     signal(SIGBUS,catch_sigbus);
-    mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     sharedMem_cmd = (struct pwm_cmd *) mmap(0, 0x1000, PROT_READ|PROT_WRITE, 
                                             MAP_SHARED, mem_fd, RCOUT_ZYNQ_PWM_BASE);
     close(mem_fd);
diff --git a/libraries/AP_HAL_Linux/Storage.cpp b/libraries/AP_HAL_Linux/Storage.cpp
index 04060e2669..e111ed88dd 100644
--- a/libraries/AP_HAL_Linux/Storage.cpp
+++ b/libraries/AP_HAL_Linux/Storage.cpp
@@ -35,7 +35,7 @@ void Storage::_storage_create(void)
 {
     mkdir(STORAGE_DIR, 0777);
     unlink(STORAGE_FILE);
-    int fd = open(STORAGE_FILE, O_RDWR|O_CREAT, 0666);
+    int fd = open(STORAGE_FILE, O_RDWR|O_CREAT|O_CLOEXEC, 0666);
     if (fd == -1) {
         AP_HAL::panic("Failed to create " STORAGE_FILE);
     }
@@ -57,10 +57,10 @@ void Storage::_storage_open(void)
     }
 
     _dirty_mask = 0;
-    int fd = open(STORAGE_FILE, O_RDWR);
+    int fd = open(STORAGE_FILE, O_RDWR|O_CLOEXEC);
     if (fd == -1) {
         _storage_create();
-        fd = open(STORAGE_FILE, O_RDWR);
+        fd = open(STORAGE_FILE, O_RDWR|O_CLOEXEC);
         if (fd == -1) {
             AP_HAL::panic("Failed to open " STORAGE_FILE);
         }
@@ -80,7 +80,7 @@ void Storage::_storage_open(void)
     if (ret != sizeof(_buffer)) {
         close(fd);
         _storage_create();
-        fd = open(STORAGE_FILE, O_RDONLY);
+        fd = open(STORAGE_FILE, O_RDONLY|O_CLOEXEC);
         if (fd == -1) {
             AP_HAL::panic("Failed to open " STORAGE_FILE);
         }
@@ -137,7 +137,7 @@ void Storage::_timer_tick(void)
     }
 
     if (_fd == -1) {
-        _fd = open(STORAGE_FILE, O_WRONLY);
+        _fd = open(STORAGE_FILE, O_WRONLY|O_CLOEXEC);
         if (_fd == -1) {
             return;
         }
diff --git a/libraries/AP_HAL_Linux/ToneAlarm.cpp b/libraries/AP_HAL_Linux/ToneAlarm.cpp
index e3f3e49cad..8a692c2b41 100644
--- a/libraries/AP_HAL_Linux/ToneAlarm.cpp
+++ b/libraries/AP_HAL_Linux/ToneAlarm.cpp
@@ -38,9 +38,9 @@ bool ToneAlarm::tune_repeat[TONE_NUMBER_OF_TUNES] = {false,true,false,false,fals
 
 ToneAlarm::ToneAlarm()
 {
-    period_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/period",O_WRONLY);
-    duty_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/duty",O_WRONLY);
-    run_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/run",O_WRONLY);
+    period_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/period",O_WRONLY|O_CLOEXEC);
+    duty_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/duty",O_WRONLY|O_CLOEXEC);
+    run_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/run",O_WRONLY|O_CLOEXEC);
 
     tune_num = -1;                    //initialy no tune to play
     tune_pos = 0;
diff --git a/libraries/AP_HAL_Linux/VideoIn.cpp b/libraries/AP_HAL_Linux/VideoIn.cpp
index cf7378b962..dc7e574d81 100644
--- a/libraries/AP_HAL_Linux/VideoIn.cpp
+++ b/libraries/AP_HAL_Linux/VideoIn.cpp
@@ -68,7 +68,7 @@ bool VideoIn::open_device(const char *device_path, uint32_t memtype)
 
     _fd = -1;
     _buffers = nullptr;
-    _fd = open(device_path, O_RDWR);
+    _fd = open(device_path, O_RDWR|O_CLOEXEC);
     _memtype = memtype;
     if (_fd < 0) {
         hal.console->printf("Error opening device %s: %s (%d).\n",
diff --git a/libraries/AP_HAL_Linux/qflight/dsp_functions.cpp b/libraries/AP_HAL_Linux/qflight/dsp_functions.cpp
index a6176572eb..e829d6227f 100644
--- a/libraries/AP_HAL_Linux/qflight/dsp_functions.cpp
+++ b/libraries/AP_HAL_Linux/qflight/dsp_functions.cpp
@@ -275,7 +275,7 @@ int qflight_UART_open(const char *device, int32_t *_fd)
         return -1;
     }
     struct uartbuf &b = uarts[num_open_uarts];
-    int fd = open(device, O_RDWR | O_NONBLOCK);
+    int fd = open(device, O_RDWR | O_NONBLOCK|O_CLOEXEC);
     if (fd == -1) {
         return -1;
     }