It is estimated that 1-2.5 million U.S. women use compounded bioidentical menopausal hormone therapy (MHT). However, the proportion of American physicians prescribing compounded bioidentical hormones remains unknown. This study aims to evaluate obstetrician-gynecologists' (OB/GYNs) and family medicine physicians' decisions reflected in prescribing practices of MHT in Kansas, and level of agreement with the American College of Obstetricians and Gynecologists (ACOG) recommendations. An Internet-based 38-item survey was electronically disseminated to OB/GYNs and family medicine physicians identified through the Kansas State Board of Healing Arts licensure list. Out of 1349 physicians contacted, 164 (12.2%) responded to the survey. There were 128 (9.5%) responses included in the final analysis. In the past year, 96.1% (123/128) of respondents prescribed conventional MHT, 93.0% (119/128) prescribed Food and Drug Administration (FDA)-approved bioidentical MHT, and 66.1% (84/127) prescribed compounded bioidentical MHT. Of factors influencing MHT-prescribing practices, FDA regulation was not important to 16.7% (21/126) of physicians, whereas customization was important to 68.5% (87/127). There was a significant difference between specialties, 37.7% of OB/GYNs compared with 56.9% of family medicine physicians, regarding the ACOG statement that "patients should be counseled that conventional MHT is more appropriate than compounded preparations" (p = 0.031). Respondents disagreed with ACOG regarding the statements that "the practice of compounding makes it difficult to identify the active agent responsible for various effects" (41.0% of OB/GYNs and 34.8% of family medicine physicians) and "the practice of custom blending commercially available drug products lacks both a strong biological rationale and medical evidence for effectiveness" (36.1% of OB/GYNs and 37.9% of family medicine physicians). Prescribing practices for MHT vary between specialties. This study identifies a meaningful level of disagreement with ACOG recommendations regarding prescription of compounded rather than FDA-approved MHT. Further research is needed to better understand this level of discordance.