Objective This study aimed to investigate follicle-stimulating hormone receptor (FSHR) polymorphisms (Thr307Ala and Asn680Ser), estrogen receptor 1 (ESR1) polymorphisms (PvuII and XbaI), and ESR2 polymorphisms (RsaI and AluI) in Turkish women with follicle-stimulating hormone (FSH) and anti-Mullerian hormone (AMH) discordance. Method Genotyping was performed in 60 patients aged 21-35 with FSH-AMH discordance and/or low ovarian reserve and 20 age-matched controls with normal FSH and AMH levels. The patients were investigated in four groups of 20 women according to their FSH and AMH levels. Groups 1, 2, 3, and 4 were as follows: normal FSH and low AMH levels, normal AMH and high FSH levels, high FSH and low AMH levels, and normal FSH and AMH levels. Genomic DNA was obtained from 3 cc peripheral blood, and polymorphisms were analyzed using TaqMan genotyping assays. Relations between groups of categorical variables were analyzed with a chi-square test. Differences between the groups were assessed using a student's t-test or Mann-Whitney U test. Results Women with discordant FSH and AMH levels (group 1 and group 2) were not statistically different from women with concordant FSH and AMH levels (group 3 and group 4) in terms of FSHR, ESR1, and ER2 single nucleotide polymorphisms (SNPs). Body mass index (BMI) was statistically significant between groups 1 and 2 as well as groups 2 and 3 (p = 0.004). Conclusions This study showed that FSHR, ESR1, and ESR2 SNPs have not had any effect on AMH-FSH discordance in reproductive age Turkish women.