Abstract Male factor infertility (MFI) is involved in half of the cases of couple infertility. The follicle‐stimulating hormone (FSH) therapy is considered efficient to improve semen parameters and pregnancy rate in patients with idiopathic MFI, following the lesson learned from hypogonadotropic hypogonadism. However, while in patients with hypogonadotropic hypogonadism FSH therapy, in combination with human chorionic gonadotropin (hCG), is a well‐established treatment, in patients with MFI the effects of the FSH therapy are variable and unpredictable. The FSH therapy in MFI should be a personalized treatment, tailored on the characteristics of the male patient and the couple. The pivotal aspect is the accurate identification of patients who might benefit from such treatment (responders) from those who might not (nonresponders). To date, selection of patients to be treated is based on history, physical examination, semen analysis, and hormonal assessment. However, these parameters cannot adequately identify a priori responder patients. Furthermore, tailored management should include pharmacological adaptation (dosage and duration of the therapy), as happens during ovarian hyperstimulation in assisted reproductive technologies. In a fully personalized therapy, pharmacogenetic factors must be considered. In this paper, we describe the evidence dealing with the pharmacogenetics of the FSH therapy in MFI, presenting the physiological and physiopathological basis and the pharmacogenetics studies dealing with effects of polymorphisms in the beta‐subunit of FSH ( FSHB ) and the FSH receptor ( FSHR ) gene. According to the evidence so far available, genetic evaluation of FSHB and FSHR is recommended only for research purposes, since the data are not conclusive and even contrasting. Furthermore, the evidence so far is derived from quite small studies with different endpoints considered and relatively few cases. Better studies that consider the combined effect of several FSHB and FSHR gene polymorphisms, together with clinical, biochemical, seminal and testicular cytology, are necessary to develop an algorithm that might predict the response to the FSH treatment.