IntroductionThere is growing evidence that genetic changes are present in as many as 10% of infertile females. The Kisspeptin system plays a critical regulatory role in female reproductive functions. However, the extent of its role is not yet evident in primary infertility.ObjectiveThis study investigated the relative gene expression levels of Kisspeptin, KISS1, and KISS1R in primary infertile and fertile Nigerian females.Materials and MethodsThis is a case‐control study of 50 fertile and 54 primary infertile Nigerian females (20 to 40 years) attending the gynecology and family planning clinics of University College Hospital, Nigeria, and met the study’s inclusion criteria between August and November 2020. Basic clinical and sociodemographic information was collected from each participant using a clinical proforma. Five ml of blood samples were also collected by venepuncture from both the cases and control subjects for Kisspeptin, KISS1, and KISS1R genes analysis, using ELISA and RT‐qPCR techniques.ResultsBMI of cases was significantly different from the study controls, though both are still in the overweight category (27.98±0.87 vs. 28.18±0.59; p=0.004). Menarcheal age was not significantly different (p=0.573) but shows a significant strong association with ovarian factor infertility (p=0.008, χ2=13.839, φc= 0.458) and tubal factor infertility (p=0.025, χ2=11.111; φc=0.527). There is no change in the relative expression of Kisspeptin, Kiss1, and Kiss1R genes (P>0.05). However, Kisspeptin levels in primary infertile women showed a weak negative correlation (r = ‐.305; p=0.039) and a good predictive model for Kiss1 gene expression (p=0.001; r=0.458).ConclusionFemales with primary infertility may present with overweight in no significantly different way than fertile females. Changes in the Kisspeptin levels and relative expressions of Kiss1 and Kiss1R may not be useful in diagnosing primary infertility. Menarcheal age should be investigated as an additional diagnostic indicator for tubal and ovarian factor infertility for primary infertile women.SignificanceChanges in the Kisspeptin system alone may not explain the primary female infertility due to the complexity of the disease. A look into the role of the Kisspeptin system in the specific causative factors of primary female infertility could be more revealing.