Coincidence engines follow two main implementation flows: timestamp based systems and AND-gate based systems. The latter have been more widespread in recent years because of its lower cost and high efficiency. However, they are highly dependent on the selected electronic components, they have limited flexibility once assembled and they are customized to fit a specific scanner's geometry. Timestamp based systems are gathering more attention lately, especially with high channel count fully digital systems. These new systems must however cope with important singles count rates. One option is to record every detected event and postpone coincidence detection offline. For daily use systems, a real time engine is preferable because it dramatically reduces data volume and hence image preprocessing time and raw data management. This paper presents the timestamp based coincidence engine for the LabPET™, a small animal PET scanner with up to 4608 individual readout avalanche photodiode channels. The engine can handle up to 100 million single events per second and has extensive flexibility because it resides in programmable logic devices. It can be adapted for any detector geometry or channel count, can be ported to newer, faster programmable devices and can have extra modules added to take advantage of scanner-specific features. Finally, the user can select between full processing mode for imaging protocols and minimum processing mode to study different approaches for coincidence detection with offline software. © 2010 IEEE.