Objective: To compare two types of osteoporosis treatment for genotoxicity by using sister chromatid exchange (SCE) frequencies. Method: Fifty-seven women, aged between 40 and 64 years, composed the population in the study. SCE values of patients under estrogen replacement therapy (ERT) or alendronate therapy were compared to controls who never used any drugs for osteoporosis, Result: The difference between the SCE values of women taking ERT and control women was found to be statistically significant (P < 0.05). The difference between women taking alendronate and untreated controls was not statistically significant. Conclusion: Our results indicate that alendronate does not have genotoxic effects based on SCE frequency, while ERT increases SCE frequencies; (C) 2000 International Federation of Gynecology and Obstetrics. All rights reserved.