Toxicologic pathology is the art of assessment of potential adverse effects at the tissue level in pre-clinical studies. In the case of biomaterials and medical devices, the toxicologic pathologists assess the safety (biocompatibility) and efficacy (conditions of the use) of the implantable materials. Proper assessment of biocompatibility of biomaterials is of utmost importance, since it helps to determine their safety after implantation in humans. Biomaterial-related toxicity can be attributed to several factors, including for example leachable compounds from the material leading to thrombosis or carcinogenesis, or biodegradation of the material causing changes in its physical and compatibility properties. Evaluation of biocompatibility and biofunctionality involves assessment of cytotoxicity, allergic responses, irritation, inflammation and systemic and chronic toxicity. In many of these assessments, the toxicologic pathologist has an important role in determining product safety and potential toxicity. In this article, we review the special needs for proper toxicologic pathology assessment of biomaterials and degradable polymers. We review common adverse effects expected with biomaterials and describe their pathological picture and their clinical relevance. We also introduce a novel compact MR imaging technology as a tool for assessing biocompatibility and efficacy of implanted biodegradable materials, since it allows for the longitudinal imaging and quantification of inflammation in vivo caused by the device implantation, and enabling general inspection of shape, location and integrity of the device in vivo. Since the MR imaging technique is non-invasive, the effects of the implantable device can be monitored longitudinally in the same animal without perturbation of the pathology. Copyright © 2014 John Wiley & Sons, Ltd.