Context: Rural primary care is a complex environment in which multiple patient safety challenges can arise. To make progress in improving safety with limited resources, each practice needs to identify those safety problems that pose the greatest threat to patients and focus efforts on these. Purpose: To describe and field-test a novel approach to prioritizing safety problems in rural primary care based on the method of Failure Modes and Effects Analysis. Methods: A survey instrument designed to assess perceptions of medical error frequency, severity, and cause was administered anonymously to staff of 2 rural primary care practices in New York State. Responses were converted to quantitative hazard scores, which were used to make priority rankings of safety problems. Concordance analysis was conducted. Results: Response rate was 94% at each site. Analysis yielded a list of priorities for each site. Comparison between staff groups (provider vs nursing vs administration), based on the top 10 priorities perceived by staff, showed 53% concordance at one site and 30% at the other. Concordance between sites was lower, at 20%. Conclusions: Initial field-testing of a Failure Modes and Effects Analysis approach in rural primary care suggests that it is feasible and can be used to estimate, based on staff perceptions, the greatest threats to patient safety in an individual practice so that limited resources can be focused appropriately. Higher concordance between staff within a practice than between practices lends preliminary support to the validity of the approach.