This research aims to determine the usability of the central library websites of medical sciences universities in Iran. This was a descriptive, cross-sectional study which employed a heuristic evaluation method to evaluate the usability of the websites. Three trained evaluators independently examined the 12 library websites from 11 July to 10 September 2013 using Nielsen’s usability heuristics. A list of usability problems was obtained and the severity of identified problems was determined. We identified 668 usability problems. The highest number of problems concerned ‘aesthetic and minimalist design’ (27.1%) and the lowest number concerned the ‘help and documentation’ heuristic (1%). Since the importance of libraries’ websites cannot be understated, the websites should consider the identified problems and attempt to address them.