Usability methods, such as heuristic evaluation, cognitive walk-throughs and user testing, are increasingly used to evaluate and improve the design of clinical software applications. There is still some uncertainty, however, as to how those methods can be used to support the development process and evaluation in the most meaningful manner. In this study, we compared the results of a heuristic evaluation with those of formal user tests in order to determine which usability problems were detected by both methods. We conducted heuristic evaluation and usability testing on four major commercial dental computer-based patient records (CPRs), which together cover 80% of the market for chairside computer systems among general dentists. Both methods yielded strong evidence that the dental CPRs have significant usability problems. An average of 50% of empirically-determined usability problems were identified by the preceding heuristic evaluation. Some statements of heuristic violations were specific enough to precisely identify the actual usability problem that study participants encountered. Other violations were less specific, but still manifested themselves in usability problems and poor task outcomes. In this study, heuristic evaluation identified a significant portion of problems found during usability testing. While we make no assumptions about the generalizability of the results to other domains and software systems, heuristic evaluation may, under certain circumstances, be a useful tool to determine design problems early in the development cycle.