Background Many residency programs do not accept the Comprehensive Osteopathic Medical Licensing Examination (COMLEX-USA) alone for osteopathic applicants. Furthermore, among those programs that do accept the COMLEX-USA, it is unknown how programs scale their minimum COMLEX-USA scores compared to their minimum United States Medical Licensing Examination (USMLE) scores. Objective Our objective was to examine the variation of relative within-program differences between minimum USMLE Step and COMLEX-USA Level scores required for consideration by United States residency programs. Methods We performed a cross-sectional analysis of the Fellowship and Residency Electronic Interactive Database Access (FREIDA) database from April 2023, including the 10 specialties with the most training spots in 2022. These specialties were internal medicine, family medicine, pediatrics, emergency medicine, psychiatry, surgery, anesthesiology, obstetrics-gynecology, orthopedic surgery, and neurology. Within-program differences were calculated by subtracting the minimum USMLE Step 1 and 2 scores from the converted minimum USMLE Step 1 and 2 scores calculated from the minimum COMLEX-USA Level 1 and 2 scores using two conversion tools. We present differences as medians with interquartile ranges (IQR). Additionally, we report the proportion of programs with greater than 10-point differences for each step (1 and 2). Results Of the 3,364 accredited programs from the examined specialties, we included 1,477 in the Step 1 analysis and 1,227 in the Step 2 analysis with complete data. The median within-program difference between the minimum Step 1 score and the predicted Step 1 score was 12.0 (IQR 2.0, 17.0) using the Barnum and colleagues' conversion tool and -1.7 (IQR -6.2, 6.3) using the Smith and colleagues' tool. The median differences for Step 2 were 2.0 (IQR -8.0, 12.0) and -6.5 (IQR -13.9, -1.5) for each tool, respectively. Using the Barnum and Smith conversion tools, 937 (63%) and 435 (29%) programs had a greater than 10-point Step 1 score difference, respectively. Similarly, for Step 2, 564 (46%) and 515 (42%) programs had a greater than 10-point difference with each conversion tool. Conclusion There is wide variation in the within-program differences between minimum USMLE and predicted minimum USMLE (from COMLEX-USA) scores. Many programs have greater than 10-point differences, which may be a source of bias in osteopathic applicant selection.