Accreditation of Post-Graduate Medical Education permits medical institutions to train residents, allowing them to achieve specialist certification. An accreditation system usually employs several tools such as site-visits, information gathering and occasionally self-evaluation, to determine adherence to pre-defined standards. The Scientific Council of the Israeli Medical Association is entrusted by law on this accreditation system in Israel. In our article, we briefly review the Post-Graduate Medical Education accreditation system in Israel and a number of pivotal challenges faced by the Scientific Council in this field in the 21st century. These challenges include the adaptation to different medical settings such as community based clinics and medical arrays, the adaptation of tools used for accreditation, new methods for up to date information gathering and updated structure of site-visit teams. A significant future challenge will be adapting the accreditation system to the new Competency Based Medical Education model of residency promoted in Israel by the Scientific Council.