A prerequisite for a Global Positioning System (GPS) attitude determination is to calculate baselines between antennae with accuracy at the millimetre level simultaneously. However, in order to have a low cost attitude determination system, a set of Commercial-Off-The-Shelf (COTS) receivers with separate clocks are used. In this case, if the receiver clocks are not precisely synchronized, the baseline vector between antennae will be calculated from the GPS signals received at different times. This can be a significant error source for high-kinematic applications. In this paper, two equivalent and effective approaches are developed to compensate this significant bias for baseline estimation and attitude determination. Test results using real airborne GPS data demonstrate that the receiver time misalignment between the two receivers can result in a 5 cm baseline offset for an aircraft with a 50 m/s velocity; the corresponding attitude errors can reach about 0·50° in yaw and 0·10° in pitch respectively for the attitude determination system with a baseline length of 3·79 m. With the proposed methods, these errors can be effectively eliminated.