BACKGROUND: The timing of prophylactic antibiotic administration is a patient safety outcome that is recurrently tracked and reported. The interpretation of these data has important implications for patient safety practices. However, diverse data collection methods and approaches to analysis impede knowledge building in this field. This paper makes explicit several challenges to quantifying the timing of prophylactic antibiotics that we encountered during a recent study and offers a suggested protocol for resolving these challenges. CHALLENGES: Two clear challenges manifested during the data extraction process: the actual classification of antibiotic timing, and the additional complication of multiple antibiotic regimens with different timing classifications in a single case. A formalized protocol was developed for dealing with incomplete, ambiguous and unclear documentation. A hierarchical coding system was implemented for managing cases with multiple antibiotic regimens. INTERPRETATION: Researchers who are tracking prophylactic antibiotic timing as an outcome measure should be aware that documentation of antibiotic timing in the patient chart is frequently incomplete and unclear, and these inconsistencies should be accounted for in analyses. We have developed a systematic method for dealing with specific problematic patterns encountered in the data. We propose that the general adoption of a systematic approach to analysis of this type of data will allow for cross-study comparisons and ensure that interpretation of results is on the basis of timing practices rather than documentation practices.