Using Arduino Uno as ISP to program Mega 2560 I'm trying to use Arduino Uno as ISP to program Arduino Mega 2560 using this Pin connections (Uno->Mega):

slave reset: 10:       ->        RESET on target

MOSI:        11:      ->           51

MISO:        12:      ->         50

SCK:         13:      ->        52

It runs perfectly when I "Burn Bootloader" from Arduino IDE and LED starts blinking on target. So I assume my pin connections are correct.

However, when I open the Blink example and perform "Upload Using Programmer" in Sketch tab after choosing "Arduino as ISP" in Tools>Programmer it uploads the code but LED on Mega doesn't blink.

I'm afraid that I have problem in my Mega Bootloader hex file and think it's not configuring Pin 13 as a LED pin. But in this case I shouldn't have seen the led blinking after burning the bootloader. 

What am I missing here? I appreciate your help.
-Bex
Find the file called "boards.txt" located in your Arduino installation directory. In my case, the path is "arduino-1.6.5/hardware/arduino/avr/boards.txt". Open it with your favourite text editor and locate the ATMEGA2560 section. (not in notepad, it breaks the file format, notepad++ my choice)

in boards.txt


back-up the file incase you break it,
find the line :
mega.menu.cpu.atmega2560.bootloader.high_fuses=0xD8
and change it with :
mega.menu.cpu.atmega2560.bootloader.high_fuses=0xD9


Source : http://soc.ninja/documentation/programming-atmega2560-with-arduino-uno-or-mega/#rating-74