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From September 21st-23rd 2009, the Clinical Investigator Trainee Association of Canada - Association des cliniciens-chercheurs en formation du Canada (CITAC-ACCFC) and the Canadian Society for Clinician Investigators (CSCI), held their annual conference in Ottawa. Participants included clinician investigators and trainees from across the country. The conference featured many excellent guest speakers including this year's recipient of the Henry G. Friesen International Prize in Health Research, Sir John Bell. There were several forums focusing on professional development, with topics such as "sustaining the clinician investigator in Canada", "succeeding as a clinician investigator", and "collaborating internationally with MD+ trainees", alongside networking opportunities to help establish relationships with potential mentors and collaborators. Further, the CSCI-CITAC annual conference featured some of the cutting edge research that MD+ trainees throughout Canada are engaged in. Trainees presented their research either at the Young Investigators Forum poster session or at the oral plenary. This scientific overview aims to highlight some of the research presented by trainees at the annual conference. The broad themes of scientific interest included topics from both basic science and clinical research. In this article, we summarize some of the major research questions that are being investigated by clinician-investigator trainees in the following areas: neurological sciences, cell biology, medicine, immunology, obstetrics, gynecology, neonatology, orthopedics, rheumatology, and public health.