Abstract Objectives Hormonal disturbances during menopause are an established influencing factor on bone health, but the role of controlled ovarian hyperstimulation for fertility treatment remains unclear. To evaluate the influence of ovarian stimulation on bone metabolism with particular regard to serum follicle-stimulating hormone (FSH) levels this prospective observational study was conducted. Methods A total of 71 women underwent controlled ovarian hyperstimulation with recombinant FSH (rFSH) or human menopausal gonadotropin (HMG) (FSH + LH) administered in individual doses, with gonadotropin-releasing hormone (GnRH) agonist down-regulation initiated in the luteal phase of the previous cycle. At four time points (start of down-regulation [T1], start of ovarian stimulation [T2], oocyte retrieval [T3] and luteal phase of the stimulation cycle [T4]), luteinizing hormone (LH), FSH, estradiol (E2), osteocalcin (OC), bone-specific alkaline phosphatase (BAP), as well as the bone resorption markers β-isomerized C-terminal telopeptide of type I collagen (β-CTX) and tartrate-resistant acid phosphatase (TRACP) were measured. Results The cyclic variations in FSH levels had a positive effect on the concentration profile of the bone resorption marker β-CTX (p=0.0001). Supraphysiologic estradiol levels showed a negative association with osteocalcin concentrations (p=0.017), and significantly lower OC and TRACP levels were observed at T4 compared to T1. By group comparison, women treated with rFSH presented with a higher bone turnover than the HMG group at the end of a stimulation cycle (T4). Conclusions Our results show that FSH is a significant influencing factor of bone metabolism. Overall, there was no evidence of enhanced bone resorption under short-term ovarian stimulation therapy. Further studies with bigger sample sizes are warranted to validate these results.