One of the determinants of the medical student's behaviour is the medical school learning environment. The aim of this research was to identify the instruments used to measure the educational environment in health professions education and to assess their validity and reliability. We performed an electronic search in the medical literature analysis and retrieval system online (MEDLINE) and Timelit (Topics in medical education) databases through to October 2008. The non-electronic search (hand searching) was conducted through reviewing the references of the retrieved studies and identifying the relevant ones. Two independent authors read, rated and selected studies for the review according to the pre-specified criteria. The inter-rater agreement was measured with Kappa coefficient. Seventy-nine studies were included with the Kappa coefficient of 0.79, which demonstrated a reliable process, and 31 instruments were extracted. The Dundee Ready Education Environment Measure, Postgraduate Hospital Educational Environment Measure, Clinical Learning Environment and Supervision and Dental Student Learning Environment Survey are likely to be the most suitable instruments for undergraduate medicine, postgraduate medicine, nursing and dental education, respectively. As a valid and reliable instrument is available for each educational setting, a study to assess the educational environment should become a part of an institution's good educational practice. Further studies employing a wider range of databases with more elaborated search strategies will increase the comprehensiveness of the systematic review.