diff --git a/LUFA/ManPages/ChangeLog.txt b/LUFA/ManPages/ChangeLog.txt
index c708b3e7684e6e00161d41dd4553e7991cfe1367..df74a7c08ceb2a948ae72db9e2023487b498856e 100644
--- a/LUFA/ManPages/ChangeLog.txt
+++ b/LUFA/ManPages/ChangeLog.txt
@@ -43,6 +43,8 @@
   *   - Changed over library projects to use the new general ring buffer library driver module
   *   - Added new high level TWI packet read/write commands, altered behaviour of the TWI_StartTransmission() function
   *   - Changed TempDataLogger project's DS1307 driver to simplify the function interface and prevent a possible race condition
+  *   - Changed AVRISP-MKII project to use the Watchdog interrupt for command timeouts, to reduce CPU usage and free timer 0
+  *     for other uses
   *
   *  <b>Fixed:</b>
   *  - Core:
diff --git a/LUFA/ManPages/LUFAPoweredProjects.txt b/LUFA/ManPages/LUFAPoweredProjects.txt
index 285252cb8e8f22c646c95f00d0e116b171faf6af..52ec1358ca144e23e49bc9f1153077e58b5f6d34 100644
--- a/LUFA/ManPages/LUFAPoweredProjects.txt
+++ b/LUFA/ManPages/LUFAPoweredProjects.txt
@@ -88,6 +88,7 @@
  *  - Retrode, a USB Games Console Cartridge Reader: http://www.retrode.org
  *  - USBTINY-MKII, an AVRISP-MKII Clone AVR Programmer: http://tom-itx.dyndns.org:81/~webpage/boards/USBTiny_Mkii/USBTiny_Mkii_index.php
  *  - XMEGA Development Board, using LUFA as an On-Board Programmer: http://xmega.mattair.net/
+ *  - Zeptoprog, a multifunction AVR programmer: http://www.mattairtech.com/index.php/featured/zeptoprog.html
  *
  *  \section Sec_LUFAPublications Publications Mentioning LUFA
  *  - Elektor Magazine, "My First AVR-USB" by Antoine Authier (feature), January 2010 Issue
diff --git a/Projects/AVRISP-MKII/Lib/ISP/ISPProtocol.c b/Projects/AVRISP-MKII/Lib/ISP/ISPProtocol.c
index 9a732dea2d65c5f3b59dae8179f2d6481f1406cb..27e1cc96ca589521ddd39d0b2a59d52cd5fd2dde 100644
--- a/Projects/AVRISP-MKII/Lib/ISP/ISPProtocol.c
+++ b/Projects/AVRISP-MKII/Lib/ISP/ISPProtocol.c
@@ -68,15 +68,14 @@ void ISPProtocol_EnterISPMode(void)
 	ISPProtocol_DelayMS(Enter_ISP_Params.ExecutionDelayMS);
 	ISPTarget_EnableTargetISP();
 
+	ISPTarget_ChangeTargetResetLine(true);
+
 	/* Continuously attempt to synchronize with the target until either the number of attempts specified
 	 * by the host has exceeded, or the the device sends back the expected response values */
-	while (Enter_ISP_Params.SynchLoops-- && (ResponseStatus != STATUS_CMD_OK) && TimeoutTicksRemaining)
+	while (Enter_ISP_Params.SynchLoops-- && (ResponseStatus != STATUS_CMD_OK) && !(TimeoutExpired))
 	{
 		uint8_t ResponseBytes[4];
 
-		ISPTarget_ChangeTargetResetLine(true);
-		ISPProtocol_DelayMS(Enter_ISP_Params.PinStabDelayMS);
-
 		for (uint8_t RByte = 0; RByte < sizeof(ResponseBytes); RByte++)
 		{
 			ISPProtocol_DelayMS(Enter_ISP_Params.ByteDelay);
@@ -92,6 +91,7 @@ void ISPProtocol_EnterISPMode(void)
 		{
 			ISPTarget_ChangeTargetResetLine(false);
 			ISPProtocol_DelayMS(Enter_ISP_Params.PinStabDelayMS);
+			ISPTarget_ChangeTargetResetLine(true);
 		}
 	}
 
@@ -509,7 +509,7 @@ void ISPProtocol_SPIMulti(void)
  */
 void ISPProtocol_DelayMS(uint8_t DelayMS)
 {
-	while (DelayMS-- && TimeoutTicksRemaining)
+	while (DelayMS-- && !(TimeoutExpired))
 	  _delay_ms(1);
 }
 
diff --git a/Projects/AVRISP-MKII/Lib/ISP/ISPTarget.c b/Projects/AVRISP-MKII/Lib/ISP/ISPTarget.c
index 624d591722e6c2437e28c5d4b01745b8da27df74..88b33fc6541b0cb6b11149fa22ccaa55bf3f9739 100644
--- a/Projects/AVRISP-MKII/Lib/ISP/ISPTarget.c
+++ b/Projects/AVRISP-MKII/Lib/ISP/ISPTarget.c
@@ -250,7 +250,7 @@ uint8_t ISPTarget_TransferSoftSPIByte(const uint8_t Byte)
 
 	TCNT1  = 0;
 	TCCR1B = ((1 << WGM12) | (1 << CS11));
-	while (SoftSPI_BitsRemaining && TimeoutTicksRemaining);
+	while (SoftSPI_BitsRemaining && !(TimeoutExpired));
 	TCCR1B = 0;
 
 	return SoftSPI_Data;
@@ -292,9 +292,9 @@ uint8_t ISPTarget_WaitWhileTargetBusy(void)
 		ISPTarget_SendByte(0x00);
 		ISPTarget_SendByte(0x00);
 	}
-	while ((ISPTarget_ReceiveByte() & 0x01) && TimeoutTicksRemaining);
+	while ((ISPTarget_ReceiveByte() & 0x01) && !(TimeoutExpired));
 
-	return TimeoutTicksRemaining ? STATUS_CMD_OK : STATUS_RDY_BSY_TOUT;
+	return (TimeoutExpired) ? STATUS_RDY_BSY_TOUT : STATUS_CMD_OK;
 }
 
 /** Sends a low-level LOAD EXTENDED ADDRESS command to the target, for addressing of memory beyond the
@@ -344,9 +344,9 @@ uint8_t ISPTarget_WaitForProgComplete(const uint8_t ProgrammingMode,
 				ISPTarget_SendByte(PollAddress >> 8);
 				ISPTarget_SendByte(PollAddress & 0xFF);
 			}
-			while ((ISPTarget_TransferByte(0x00) == PollValue) && TimeoutTicksRemaining);
+			while ((ISPTarget_TransferByte(0x00) == PollValue) && !(TimeoutExpired));
 
-			if (!(TimeoutTicksRemaining))
+			if (TimeoutExpired)
 			 ProgrammingStatus = STATUS_CMD_TOUT;
 
 			break;
diff --git a/Projects/AVRISP-MKII/Lib/V2Protocol.c b/Projects/AVRISP-MKII/Lib/V2Protocol.c
index f6ea477097a905901615850170353ef8d37d6982..b510d43a6c7c69335ee4e5d876256069620b4a10 100644
--- a/Projects/AVRISP-MKII/Lib/V2Protocol.c
+++ b/Projects/AVRISP-MKII/Lib/V2Protocol.c
@@ -44,10 +44,10 @@ bool MustLoadExtendedAddress;
 
 
 /** ISR to manage timeouts whilst processing a V2Protocol command */
-ISR(TIMER0_COMPA_vect, ISR_NOBLOCK)
+ISR(WDT_vect, ISR_BLOCK)
 {
-	if (TimeoutTicksRemaining)
-	  TimeoutTicksRemaining--;
+	TimeoutExpired = true;
+	wdt_disable();
 }
 
 /** Initialises the hardware and software associated with the V2 protocol command handling. */
@@ -60,11 +60,6 @@ void V2Protocol_Init(void)
 	ADC_StartReading(ADC_REFERENCE_AVCC | ADC_RIGHT_ADJUSTED | VTARGET_ADC_CHANNEL_MASK);
 	#endif
 
-	/* Timeout timer initialization (10ms period) */
-	OCR0A  = (((F_CPU / 1024) / 100) - 1);
-	TCCR0A = (1 << WGM01);
-	TIMSK0 = (1 << OCIE0A);
-
 	V2Params_LoadNonVolatileParamValues();
 	
 	#if defined(ENABLE_ISP_PROTOCOL)
@@ -80,9 +75,10 @@ void V2Protocol_ProcessCommand(void)
 {
 	uint8_t V2Command = Endpoint_Read_Byte();
 
-	/* Start the timeout management timer */
-	TimeoutTicksRemaining = COMMAND_TIMEOUT_TICKS;
-	TCCR0B = ((1 << CS02) | (1 << CS00));
+	/* Start the watchdog with timeout interrupt enabled to manage the timeout */
+	TimeoutExpired = false;
+	wdt_enable(WDTO_1S);
+	WDTCSR |= (1 << WDIE);
 
 	switch (V2Command)
 	{
@@ -144,8 +140,8 @@ void V2Protocol_ProcessCommand(void)
 			break;
 	}
 
-	/* Disable the timeout management timer */
-	TCCR0B = 0;
+	/* Disable the timeout management watchdog timer */
+	wdt_disable();
 
 	Endpoint_WaitUntilReady();
 	Endpoint_SelectEndpoint(AVRISP_DATA_OUT_EPNUM);
diff --git a/Projects/AVRISP-MKII/Lib/V2Protocol.h b/Projects/AVRISP-MKII/Lib/V2Protocol.h
index ed42de96ef4b1142485bf0d5761c4e4ef417f99d..8e9e6ff38ff9e84deab193413b0d6deb2912afbe 100644
--- a/Projects/AVRISP-MKII/Lib/V2Protocol.h
+++ b/Projects/AVRISP-MKII/Lib/V2Protocol.h
@@ -39,6 +39,7 @@
 	/* Includes: */
 		#include <avr/io.h>
 		#include <avr/interrupt.h>
+		#include <avr/wdt.h>
 	
 		#include <LUFA/Drivers/USB/USB.h>
 
@@ -68,8 +69,8 @@
 		/** Timeout period for each issued command from the host before it is aborted (in 10ms ticks). */
 		#define COMMAND_TIMEOUT_TICKS      100
 
-		/** Command timeout counter register, GPIOR for speed. */
-		#define TimeoutTicksRemaining      GPIOR1
+		/** Command timeout expiration flag, GPIOR for speed. */
+		#define TimeoutExpired             GPIOR1
 
 		/** MUX mask for the VTARGET ADC channel number. */
 		#define VTARGET_ADC_CHANNEL_MASK   ADC_GET_CHANNEL_MASK(VTARGET_ADC_CHANNEL)
diff --git a/Projects/AVRISP-MKII/Lib/XPROG/TINYNVM.c b/Projects/AVRISP-MKII/Lib/XPROG/TINYNVM.c
index 0322a6ec2ed0a3a81f75115e73516fe861ef57d3..49d5766085276a8c02120d8f9994cbe6dd6bf259 100644
--- a/Projects/AVRISP-MKII/Lib/XPROG/TINYNVM.c
+++ b/Projects/AVRISP-MKII/Lib/XPROG/TINYNVM.c
@@ -85,7 +85,7 @@ bool TINYNVM_WaitWhileNVMBusBusy(void)
 		uint8_t StatusRegister = XPROGTarget_ReceiveByte();
 
 		/* We might have timed out waiting for the status register read response, check here */
-		if (!(TimeoutTicksRemaining))
+		if (TimeoutExpired)
 		  return false;
 
 		/* Check the status register read response to see if the NVM bus is enabled */
@@ -110,7 +110,7 @@ bool TINYNVM_WaitWhileNVMControllerBusy(void)
 		uint8_t StatusRegister = XPROGTarget_ReceiveByte();
 
 		/* We might have timed out waiting for the status register read response, check here */
-		if (!(TimeoutTicksRemaining))
+		if (TimeoutExpired)
 		  return false;
 
 		/* Check to see if the BUSY flag is still set */
@@ -176,14 +176,14 @@ bool TINYNVM_ReadMemory(const uint16_t ReadAddress,
 	/* Send the address of the location to read from */
 	TINYNVM_SendPointerAddress(ReadAddress);
 
-	while (ReadSize-- && TimeoutTicksRemaining)
+	while (ReadSize-- && !(TimeoutExpired))
 	{
 		/* Read the byte of data from the target */
 		XPROGTarget_SendByte(TPI_CMD_SLD | TPI_POINTER_INDIRECT_PI);
 		*(ReadBuffer++) = XPROGTarget_ReceiveByte();
 	}
 
-	return (TimeoutTicksRemaining != 0);
+	return (TimeoutExpired == false);
 }
 
 /** Writes word addressed memory to the target's memory spaces.
diff --git a/Projects/AVRISP-MKII/Lib/XPROG/XMEGANVM.c b/Projects/AVRISP-MKII/Lib/XPROG/XMEGANVM.c
index eb9d0630688ce4a388099ee52452164cd8d2674c..b1fea59922582b31cf7a5ff86725ce689db59c0f 100644
--- a/Projects/AVRISP-MKII/Lib/XPROG/XMEGANVM.c
+++ b/Projects/AVRISP-MKII/Lib/XPROG/XMEGANVM.c
@@ -80,7 +80,7 @@ bool XMEGANVM_WaitWhileNVMBusBusy(void)
 		uint8_t StatusRegister = XPROGTarget_ReceiveByte();
 
 		/* We might have timed out waiting for the status register read response, check here */
-		if (!(TimeoutTicksRemaining))
+		if (TimeoutExpired)
 		  return false;
 
 		/* Check the status register read response to see if the NVM bus is enabled */
@@ -109,7 +109,7 @@ bool XMEGANVM_WaitWhileNVMControllerBusy(void)
 		uint8_t StatusRegister = XPROGTarget_ReceiveByte();
 
 		/* We might have timed out waiting for the status register read response, check here */
-		if (!(TimeoutTicksRemaining))
+		if (TimeoutExpired)
 		  return false;
 
 		/* Check to see if the BUSY flag is still set */
@@ -204,7 +204,7 @@ bool XMEGANVM_GetMemoryCRC(const uint8_t CRCCommand, uint32_t* const CRCDest)
 	for (uint8_t i = 0; i < XMEGA_CRC_LENGTH; i++)
 	  ((uint8_t*)CRCDest)[i] = XPROGTarget_ReceiveByte();
 
-	return (TimeoutTicksRemaining != 0);
+	return (TimeoutExpired == false);
 }
 
 /** Reads memory from the target's memory spaces.
@@ -236,10 +236,10 @@ bool XMEGANVM_ReadMemory(const uint32_t ReadAddress, uint8_t* ReadBuffer, uint16
 
 	/* Send a LD command with indirect access and post-increment to read out the bytes */
 	XPROGTarget_SendByte(PDI_CMD_LD | (PDI_POINTER_INDIRECT_PI << 2) | PDI_DATSIZE_1BYTE);
-	while (ReadSize-- && TimeoutTicksRemaining)
+	while (ReadSize-- && !(TimeoutExpired))
 	  *(ReadBuffer++) = XPROGTarget_ReceiveByte();
 
-	return (TimeoutTicksRemaining != 0);
+	return (TimeoutExpired == false);
 }
 
 /** Writes byte addressed memory to the target's memory spaces.
diff --git a/Projects/AVRISP-MKII/Lib/XPROG/XPROGProtocol.c b/Projects/AVRISP-MKII/Lib/XPROG/XPROGProtocol.c
index c89f94fe4de558cdf612a2a8d7345f2a421b582f..1b105ddb0efa401b03bb550d55a06e805d235602 100644
--- a/Projects/AVRISP-MKII/Lib/XPROG/XPROGProtocol.c
+++ b/Projects/AVRISP-MKII/Lib/XPROG/XPROGProtocol.c
@@ -143,6 +143,8 @@ static void XPROGProtocol_LeaveXPROGMode(void)
 	  TINYNVM_DisableTPI();
 
 	#if defined(XCK_RESCUE_CLOCK_ENABLE) && defined(ENABLE_ISP_PROTOCOL)
+	/* If the XCK rescue clock option is enabled, we need to restart it once the 
+	 * XPROG mode has been exited, since the XPROG protocol stops it after use. */
 	ISPTarget_ConfigureRescueClock();
 	#endif
 
diff --git a/Projects/AVRISP-MKII/Lib/XPROG/XPROGTarget.c b/Projects/AVRISP-MKII/Lib/XPROG/XPROGTarget.c
index 7cf62ffee313a423f7e83cdffda93da46d6315d4..0a2dee73b390fe2973865633398008a872218d5c 100644
--- a/Projects/AVRISP-MKII/Lib/XPROG/XPROGTarget.c
+++ b/Projects/AVRISP-MKII/Lib/XPROG/XPROGTarget.c
@@ -151,7 +151,7 @@ uint8_t XPROGTarget_ReceiveByte(void)
 	  XPROGTarget_SetRxMode();
 
 	/* Wait until a byte has been received before reading */
-	while (!(UCSR1A & (1 << RXC1)) && TimeoutTicksRemaining);
+	while (!(UCSR1A & (1 << RXC1)) && !(TimeoutExpired));
 
 	return UDR1;
 }