A method of determining desynchronization between a first implantable medical device and a second implantable medical device. The method includes receiving a synchronization query from the first device at the second device, that is transmitted in response to the first device detecting a predetermined transition of a first clock of the first device, the first clock having a first pulse rate. The method further includes determining a number of pulses of a second clock of the second device occurring between reception of the synchronization query and a predetermined transition of a third clock of the second device, the third clock having the first pulse rate. The second clock has a second pulse rate higher than the first pulse rate. The method further includes determining the desynchronization between the first device and the second device based on the determined number of pulses of the second clock.