This study describes the effects of using different signal synchronization methods on the tailpipe emission factors obtained by on-road tests using PEMS (Portable Emission Measurement Systems). The event-based, static correlation, and dynamics correlation methods were applied to data obtained using different PEMS. The first database included 36 cargo vehicles following the same driving cycle in various cities in Colombia. The second database involved 16 passenger transport vehicles monitored under real operating conditions in Mexico. When comparing results with the event-based synchronization method as the reference, significant differences in emission factors (>25 %) were observed. Those differences depend directly on the physical setup of the PEMS. The dynamic correlation method exhibited the best performance in all cases. When using this method, we recommend to synchronize the CO2 mass flow and fuel consumption variables first and then adjust the obtained synchronization to other species to account for differences in species diffusivities.