APD-based PET modules are provided for use in combined PET/MR imaging. Each module includes a number of independent, optically isolated detectors. Each detector includes an array of scintillator (e.g. LSO) crystals read out by an array of APDs. The modules are positioned in the tunnel of a MR scanner. Simultaneous, artifact-free images can be acquired with the APD-based PET and MR system resulting in a high-resolution and cost-effective integrated PET/MR system.