diff --git a/Makefile.base b/Makefile.base
index 9b32b31d8f94..c26d16cbdbb4 100644
--- a/Makefile.base
+++ b/Makefile.base
@@ -1,13 +1,13 @@
 ASMSRC = $(wildcard *.s)
 ASSMSRC = $(wildcard *.S)
-ASMOBJ = $(ASMSRC:%.s=$(BINDIR)%.o)
-ASMOBJ += $(ASSMSRC:%.S=$(BINDIR)%.o)
+ASMOBJ = $(ASMSRC:%.s=$(BINDIR)$(MODULE)/%.o)
+ASMOBJ += $(ASSMSRC:%.S=$(BINDIR)$(MODULE)/%.o)
 
 ifeq ($(strip $(SRC)),)
 	SRC = $(wildcard *.c)
 endif
-OBJ = $(SRC:%.c=$(BINDIR)%.o)
-DEP = $(SRC:%.c=$(BINDIR)%.d)
+OBJ = $(SRC:%.c=$(BINDIR)$(MODULE)/%.o)
+DEP = $(SRC:%.c=$(BINDIR)$(MODULE)/%.d)
 
 GIT_STRING := $(shell git describe --abbrev=4 --dirty=-`hostname`)
 GIT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
@@ -31,16 +31,19 @@ $(BINDIR)$(MODULE).a: $(OBJ) $(ASMOBJ)
 
 # compile and generate dependency info,
 # prepend path to dependency info file
-$(BINDIR)%.o: %.c
-	$(AD)$(CC) $(CFLAGS) $(INCLUDES) -c $*.c -o $(BINDIR)$*.o
+$(BINDIR)$(MODULE)/%.o: %.c
+	@mkdir -p $(BINDIR)$(MODULE)
+	$(AD)$(CC) $(CFLAGS) $(INCLUDES) -c $*.c -o $(BINDIR)$(MODULE)/$*.o
 	$(AD)$(CC) $(CFLAGS) $(INCLUDES) -MM $*.c |\
-		sed -e "1s|^|$(BINDIR)|" > $(BINDIR)$*.d
+		sed -e "1s|^|$(BINDIR)$(MODULE)/|" > $(BINDIR)$(MODULE)/$*.d
 
-$(BINDIR)%.o: %.s
-	$(AD)$(AS) $(ASFLAGS) $*.s -o $(BINDIR)$*.o
+$(BINDIR)$(MODULE)/%.o: %.s
+	@mkdir -p $(BINDIR)$(MODULE)
+	$(AD)$(AS) $(ASFLAGS) $*.s -o $(BINDIR)$(MODULE)/$*.o
 
-$(BINDIR)%.o: %.S
-	$(AD)$(CC) -c $(CFLAGS) $*.S -o $(BINDIR)$*.o
+$(BINDIR)$(MODULE)/%.o: %.S
+	@mkdir -p $(BINDIR)$(MODULE)
+	$(AD)$(CC) -c $(CFLAGS) $*.S -o $(BINDIR)$(MODULE)/$*.o
 
 # remove compilation products
 clean::
diff --git a/Makefile.modules b/Makefile.modules
index 6013c3b359d0..0627b5cccc70 100644
--- a/Makefile.modules
+++ b/Makefile.modules
@@ -1,5 +1,3 @@
-UNDEF += $(BINDIR)startup.o
-
 include $(RIOTBASE)/Makefile.pseudomodules
 include $(RIOTBASE)/Makefile.defaultmodules
 
diff --git a/boards/chronos/Makefile.include b/boards/chronos/Makefile.include
index 31258875634f..ab942e931a49 100644
--- a/boards/chronos/Makefile.include
+++ b/boards/chronos/Makefile.include
@@ -14,11 +14,13 @@ export AS = $(PREFIX)as
 export LINK = $(PREFIX)gcc
 export SIZE = $(PREFIX)size
 export OBJCOPY = $(PREFIX)objcopy
-export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)startup.o
+export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)msp430_common/startup.o
 export FLASHER = mspdebug
 export HEXFILE = $(BINDIR)$(PROJECT).hex
 export USEMODULE += msp430_common
 export FFLAGS = rf2500 "prog $(HEXFILE)"
 export OFLAGS = -O ihex
 
+export UNDEF += $(BINDIR)msp430_common/startup.o
+
 include $(RIOTBOARD)/$(BOARD)/Makefile.dep
diff --git a/boards/mbed_lpc1768/Makefile.include b/boards/mbed_lpc1768/Makefile.include
index a58a5ab2daa1..10c3b2a92ca2 100644
--- a/boards/mbed_lpc1768/Makefile.include
+++ b/boards/mbed_lpc1768/Makefile.include
@@ -25,3 +25,5 @@ export DEBUGGER_FLAGS = $(ELFFILE)
 
 export INCLUDES += -I$(RIOTBOARD)/$(BOARD)/include/ -I$(RIOTCPU)/$(CPU)/include
 export OFLAGS = -O binary
+
+export UNDEF += $(BINDIR)cpu/startup.o
diff --git a/boards/msb-430-common/Makefile.include b/boards/msb-430-common/Makefile.include
index de77bf7bafd7..303bbfa4dc57 100644
--- a/boards/msb-430-common/Makefile.include
+++ b/boards/msb-430-common/Makefile.include
@@ -29,3 +29,5 @@ export FFLAGS += "prog $(HEXFILE)"
 export USEMODULE += msp430_common
 export INCLUDES += -I$(RIOTCPU)/msp430-common/include/ -I$(RIOTBOARD)/msb-430-common/include -I$(RIOTBOARD)/msb-430-common/drivers/include
 export OFLAGS = -O ihex
+
+export UNDEF += $(BINDIR)msp430_common/startup.o
diff --git a/boards/msba2-common/Makefile.include b/boards/msba2-common/Makefile.include
index a04e399348aa..ff1eae295e32 100644
--- a/boards/msba2-common/Makefile.include
+++ b/boards/msba2-common/Makefile.include
@@ -26,3 +26,5 @@ include $(RIOTBOARD)/msba2-common/Makefile.dep
 export INCLUDES += -I$(RIOTBOARD)/msba2-common/include -I$(RIOTBOARD)/msba2-common/drivers/include
 
 export OFLAGS = -O ihex
+
+export UNDEF += $(BINDIR)cpu/startup.o
diff --git a/boards/native/Makefile.include b/boards/native/Makefile.include
index d88c4afcc775..e23dcdf11765 100644
--- a/boards/native/Makefile.include
+++ b/boards/native/Makefile.include
@@ -88,3 +88,5 @@ eval-gprof:
 
 eval-cachegrind:
 	$(CGANNOTATE) $(shell ls -rt cachegrind.out* | tail -1)
+
+export UNDEF += $(BINDIR)cpu/startup.o
diff --git a/boards/redbee-econotag/Makefile.include b/boards/redbee-econotag/Makefile.include
index 687457634b02..4d9f9736752e 100644
--- a/boards/redbee-econotag/Makefile.include
+++ b/boards/redbee-econotag/Makefile.include
@@ -28,7 +28,7 @@ export HEXFILE = $(BINDIR)/$(PROJECT).hex
 export FFLAGS = -t $(PORT) -f $(HEXFILE) -c 'bbmc -l redbee-econotag reset'
 export OFLAGS = -O binary --gap-fill=0xff
 
-export INCLUDES += -I$(RIOTCPU)/$(CPU)/include/ -I$(RIOTBOARD)/$(BOARD)/include
+export INCLUDES += -I$(RIOTCPU)/$(CPU)/include/ -I$(RIOTBOARD)/$(BOARD)/include/
 
 # un-comment once https://github.com/RIOT-OS/RIOT/issues/676 is fixed
 #ifneq (,$(filter defaulttransceiver,$(USEMODULE)))
@@ -39,3 +39,5 @@ export INCLUDES += -I$(RIOTCPU)/$(CPU)/include/ -I$(RIOTBOARD)/$(BOARD)/include
 #		USEMODULE += transceiver
 #	endif
 #endif
+
+export UNDEF += $(BINDIR)cpu/startup.o
diff --git a/boards/telosb/Makefile.include b/boards/telosb/Makefile.include
index 8a86c618f521..60cc849660e6 100644
--- a/boards/telosb/Makefile.include
+++ b/boards/telosb/Makefile.include
@@ -13,7 +13,7 @@ export AS = $(PREFIX)as
 export LINK = $(PREFIX)gcc
 export SIZE = $(PREFIX)size
 export OBJCOPY = $(PREFIX)objcopy
-export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)startup.o
+export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)msp430_common/startup.o
 export TERMPROG = $(RIOTBASE)/dist/tools/pyterm/pyterm.py
 export FLASHER = goodfet.bsl
 ifeq ($(strip $(PORT)),)
@@ -33,3 +33,5 @@ ifneq (,$(filter defaulttransceiver,$(USEMODULE)))
 		USEMODULE += transceiver
 	endif
 endif
+
+export UNDEF += $(BINDIR)msp430_common/startup.o
diff --git a/boards/wsn430-common/Makefile.include b/boards/wsn430-common/Makefile.include
index b0aa7e603659..8a2b96bdecf0 100644
--- a/boards/wsn430-common/Makefile.include
+++ b/boards/wsn430-common/Makefile.include
@@ -12,7 +12,7 @@ export AS = $(PREFIX)as
 export LINK = $(PREFIX)gcc
 export SIZE = $(PREFIX)size
 export OBJCOPY = $(PREFIX)objcopy
-export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)startup.o
+export LINKFLAGS = -mmcu=$(MCU) -lgcc $(BINDIR)msp430_common/startup.o
 export FLASHER = mspdebug
 ifeq ($(strip $(PORT)),)
     export PORT = /dev/ttyUSB0
@@ -22,3 +22,5 @@ export FFLAGS = -d $(PORT) -j uif "prog $(HEXFILE)"
 
 export INCLUDES += -I$(RIOTBOARD)/wsn430-common/include
 export OFLAGS = -O ihex
+
+export UNDEF += $(BINDIR)msp430_common/startup.o
diff --git a/cpu/arm_common/Makefile.include b/cpu/arm_common/Makefile.include
index 2314e4623983..2892e55f75c6 100644
--- a/cpu/arm_common/Makefile.include
+++ b/cpu/arm_common/Makefile.include
@@ -1,3 +1,3 @@
 INCLUDES += -I$(RIOTBASE)/cpu/arm_common/include/
 
-export UNDEF += $(BINDIR)syscalls.o
+export UNDEF += $(BINDIR)arm_common/syscalls.o
diff --git a/cpu/lpc1768/Makefile.include b/cpu/lpc1768/Makefile.include
index d3ef771ec2f2..bfc25dabb943 100644
--- a/cpu/lpc1768/Makefile.include
+++ b/cpu/lpc1768/Makefile.include
@@ -1,3 +1,3 @@
 INCLUDES += -I$(RIOTBASE)/cpu/lpc1768/include
 
-export UNDEF += $(BINDIR)syscalls.o
+export UNDEF += $(BINDIR)cpu/syscalls.o
diff --git a/cpu/lpc_common/Makefile.include b/cpu/lpc_common/Makefile.include
index d90912db9042..b395c4ec76c8 100644
--- a/cpu/lpc_common/Makefile.include
+++ b/cpu/lpc_common/Makefile.include
@@ -1,3 +1,3 @@
 INCLUDES += -I$(RIOTCPU)/lpc_common/include
 
-export UNDEF += $(BINDIR)lpc_syscalls.o
+export UNDEF += $(BINDIR)lpc_common/lpc_syscalls.o
diff --git a/cpu/mc1322x/Makefile.include b/cpu/mc1322x/Makefile.include
index 20f8afee4ba5..06535d8234cf 100644
--- a/cpu/mc1322x/Makefile.include
+++ b/cpu/mc1322x/Makefile.include
@@ -2,6 +2,6 @@ INCLUDES += -I$(RIOTBASE)/cpu/mc1322x/include
 
 include $(RIOTCPU)/arm_common/Makefile.include
 
-export UNDEF += $(BINDIR)mc1322x_syscalls.o
+export UNDEF += $(BINDIR)cpu/mc1322x_syscalls.o
 
 export USEMODULE += arm_common