A method to operate an electronic controlled internal combustion engine to perform on board NOx emissions level diagnostics. In one embodiment, the method may include operating the engine to maintain a predetermined temperature for a predetermined period of time, determining whether the engine operating status is stable for one of cruise control, idle engine speed, engine torque, or high idle regeneration for a predetermined period of time, cycling the EGR valve between a first position for a predetermined period of time and then in a second position for a predetermined period of time, a determining a change in engine out NOx levels to determine whether an engine component or system is malfunctioning.