Disclosed are a method and system for calculating clock offset and skew between two clocks in a computer system. The method comprises the steps of sending data packets from a first processing unit in the computer system to a second processing unit in the computer system, and sending the data packets from the second processing unit to the first processing unit. First, second, third and fourth time stamps are provided to indicate, respectively, when the packets leave the first processing unit, arrive at the second processing unit, leave the second processing unit, and arrive at the first processing unit. The method comprises the further steps of defining a set of backward delay points using the fourth time stamps, and calculating a clock offset between clocks on the first and second processing units and clock skews of said clocks using said set of backward delay points.