diff --git a/cmake/cygwin_cygpath.cmake b/cmake/cygwin_cygpath.cmake
new file mode 100644
index 0000000000..238cfba93a
--- /dev/null
+++ b/cmake/cygwin_cygpath.cmake
@@ -0,0 +1,50 @@
+############################################################################
+#
+# Copyright (c) 2017 PX4 Development Team. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in
+#    the documentation and/or other materials provided with the
+#    distribution.
+# 3. Neither the name PX4 nor the names of its contributors may be
+#    used to endorse or promote products derived from this software
+#    without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
+# AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+############################################################################
+
+#=============================================================================
+#
+#	Converts a cygwin path (/cygdrive/c/...) to a mixed windows path (C:/...)
+#
+#	It is called on every platform but only adjusts the output when
+#	called inside the cygwin environment.
+#
+
+macro (CYGPATH _path _cygpath)
+	if (CMAKE_HOST_SYSTEM_NAME STREQUAL CYGWIN)
+		EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+		OUTPUT_VARIABLE ${_cygpath})
+		string (STRIP ${${_cygpath}} ${_cygpath})
+	else()
+		set(${_cygpath} ${${_path}})
+	endif ()
+endmacro (CYGPATH)
diff --git a/platforms/nuttx/CMakeLists.txt b/platforms/nuttx/CMakeLists.txt
index cd9cf2cd1d..732293808a 100644
--- a/platforms/nuttx/CMakeLists.txt
+++ b/platforms/nuttx/CMakeLists.txt
@@ -1,4 +1,5 @@
 include(common/px4_upload)
+include(cygwin_cygpath)
 
 if (NOT FW_NAME)
 	set(FW_NAME ${CONFIG}.elf)
@@ -35,9 +36,13 @@ if (NOT LD_SCRIPT)
 	set(LD_SCRIPT ld.script)
 endif()
 
+# only in the cygwin environment: convert paths for
+# linker script, map file and binary output to mixed windows paths (C:/...)
+CYGPATH(PX4_BINARY_DIR PX4_BINARY_DIR_CYG)
+
 target_link_libraries(${FW_NAME}
-	-T${PX4_BINARY_DIR}/NuttX/nuttx/configs/${BOARD}/scripts/${LD_SCRIPT}
-	-Wl,-Map=${PX4_BINARY_DIR}/${CONFIG}.map
+	-T${PX4_BINARY_DIR_CYG}/NuttX/nuttx/configs/${BOARD}/scripts/${LD_SCRIPT}
+	-Wl,-Map=${PX4_BINARY_DIR_CYG}/${CONFIG}.map
 	-Wl,--warn-common
 	-Wl,--gc-sections
 	-Wl,--start-group
@@ -62,7 +67,7 @@ string(REPLACE ".elf" ".px4" fw_file ${fw_file})
 string(REPLACE "nuttx_" "" fw_file ${fw_file})
 
 add_custom_command(OUTPUT ${BOARD}.bin
-	COMMAND ${OBJCOPY} -O binary ${PX4_BINARY_DIR}/${FW_NAME} ${BOARD}.bin
+	COMMAND ${OBJCOPY} -O binary ${PX4_BINARY_DIR_CYG}/${FW_NAME} ${BOARD}.bin
 	DEPENDS ${FW_NAME}
 	)
 
diff --git a/src/drivers/px4io/CMakeLists.txt b/src/drivers/px4io/CMakeLists.txt
index dbadf15a66..d500cc77f8 100644
--- a/src/drivers/px4io/CMakeLists.txt
+++ b/src/drivers/px4io/CMakeLists.txt
@@ -43,6 +43,8 @@ px4_add_module(
 		platforms__common
 	)
 
+include(cygwin_cygpath)
+
 # include the px4io binary in ROMFS
 message(STATUS "Building and including ${config_io_board}")
 
@@ -60,9 +62,15 @@ add_custom_command(OUTPUT ${fw_io_exe}
 	COMMENT "Building ${config_io_board}"
 	USES_TERMINAL
 	)
+
+# only in the cygwin environment: convert paths for
+# binary in and output to mixed windows paths (C:/...)
+CYGPATH(fw_io_exe fw_io_exe_cyg)
+CYGPATH(fw_io_bin fw_io_bin_cyg)
+
 add_custom_command(OUTPUT ${fw_io_bin}
 	COMMAND mkdir -p ${PX4_BINARY_DIR}/ROMFS/${config_romfs_root}/extras/
-	COMMAND ${OBJCOPY} -O binary ${fw_io_exe} ${fw_io_bin}
+	COMMAND ${OBJCOPY} -O binary ${fw_io_exe_cyg} ${fw_io_bin_cyg}
 	DEPENDS ${fw_io_exe}
 	COMMENT "Copying ${config_io_board} to ROMFS extras"
 	)