This paper presents a new algorithm for estimating pulse repetition intervals (PRIs) of stagger PRI pulse trains using a 2 dimensional TDOA histogram. The PRI transform algorithm can remove harmonics of stable and jitter PRI pulse trains in a TDOA histogram. But, it is impossible for the algorithm to detect stagger PRI pulse trains because it regards frame PRIs of stagger Pulse trains as harmonics of stable PRI pulse trains. A new algorithm of this paper has an ability to distinguish stagger pulse trains from harmonics of other pulse trains and to estimate frame PRIs of detected pulse trains.