Evaluation of ovarian histology is feasible by obtaining ovarian tissue through laparoscopy; however, the role of an ovarian biopsy in an infertility workup is not widely accepted. To gain insight into the role of ovarian biopsy in reproductive medicine, we conducted a cross-sectional study in infertile patients with ovarian dysfunction and correlated follicle stimulating hormone (FSH) and estradiol serum concentrations with ovarian follicular counts. Fifty women were recruited and classified into four groups: premature ovarian failure (POF), chronic anovulation, diminished ovarian reserve, and ovulatory patients (control group). Ovarian endocrine function was assessed by the determination of FSH, luteinizing hormone, and estradiol serum concentrations and correlated with the number of follicles present in the ovarian biopsies obtained by laparoscopy. The number of ovarian follicles observed for each individual biopsy varied extensively. Patients with POF presented significantly lower counts of primordial, primary, and secondary follicles. No significant differences were found in the other groups. In the total sample, primordial follicle counts correlated inversely with serum FSH levels (r = -0.4, p = 0.003) and directly with serum estradiol levels (r = 0.5, p = 0.001) however, such associations no longer remained after adjusting by group. We conclude that ovarian biopsies do not provide additional information to the clinical-hormonal criteria previously established in the workup of infertile patients. Therefore, its use cannot be generalized in the study of infertile patients with ovarian dysfunction. In contrast, ovarian biopsies may be useful to identify patients with POF when the ovarian reserve is likely altered.