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With increasing attention to patient safety, hospitals and other clinical facilities are developing practice guidelines and protocols with the specific intent of reducing harm to patients. However, the introduction of these protocols can have unanticipated negative consequences and if followed rigidly can become disabling. We use the manual count procedure that was designed to improve patient safety by reducing the likelihood of leaving an object (e.g., needle, sponge, or instrument) inside a patient body cavity during a surgical procedure to illustrate this point. Using results from a focus group of seven operating room nurses and an observational study of nine complex operations, we show that the count protocol has unanticipated negative consequences that need to be considered in evaluating the net positive gain in patient safety. The study highlights the importance of evaluating the overall impact of proposed protocols in assessing its potential benefits to patient safety.