We are now developing two PET systems, one is multi-slice dual layer MR-compatible animal PET system: KPET I, and the other is dual layer GSO PET system for small animal: K-PET II. For these PET systems, a compact and flexible data acquisition system was developed. The data acquisition system consists of analog boards and a A-D and digital board. In the analog boards, signals from the PET detectors were weighted summed according to the position of the anodes of PSPMT. Maximum of eight analog boards can be set in an acquisition system. The weighted summed signals were fed to the A-D and digital board. In the A-D and digital board, weighted summed signals were digitized by 100MHz free running analog-to-digital (A-D) converters. The digital board also processes in real-time such as digitally integration, position calculation, position and energy look-up-table (LUT) checking, pulse shape discrimination, time stamps, and coincidence detection. Accidental coincidence was also measured by the delayed coincidence. These processing can easily be modified because the digital board was based on field programmable gate arrays (FPGAs). Coincidence data were transferred to PC and stored in list node. The total acquisition system is contained in a 14 slot compact PCI rack of which size is less than 50cm x 40cm x 50cm. The system can handle most processing needed for PET system. The system is flexible and can be applied to another PET systems by only changing the analog boards if the anode signal arrangements of PMTs are different. Because the single event acquisition is also possible, the system can be applied not only to PET systems but also to SPECT systems.