In Global Navigation Satellite Systems (GNSS) the user's position is determined measuring the time of flight of the signals broadcast from satellites, which is proportional to the distance between the user and each satellite of the constellation. Time and frequency metrology has an essential role in satellite navigation systems: since a distance can be measured from a time, any error on the measure of time leads to an error on the user's position. Hence, it is fundamental to have precise and stable atomic clocks on board satellites. Therefore the on board clock behaviour has to be continuously monitored and any malfunctioning has to be detected immediately to ensure the adequacy of the timing system to the positioning service and users' needs. This paper will describe the main methodologies for characterization of onboard clocks and their implementation in a robust software developed at INRIM and also used in the framework of the European project Galileo.