Introduction: Systemic lupus erythematosus (SLE) is an autoimmune disease that affects fertile-age women and of which treatment includes immunosuppressive agents that can affect the gonads. Objective: To evaluate the frequency of menstrual alterations in lupus patient treated with immunosuppressive agents (ISA). Patients and Methods: A total of 87 patients, aged < 40 years, were studied. The patients were followed by outpatient management and the treatment used was verified. Only organic causes of menstrual alterations were excluded from the study. The menstrual alterations were correlated with the type and time of use of different ISA. Results: Age varied from 14 to 38 years, with a mean age of 28.01 ± 5.81 years; the mean age at menarche was 13.12 ± 1.77 years and the diagnosis of SLE was at 21.40 ± 5.75 years. Corticoids were used as single therapy by 63.2% of them, for a mean time of 6.11 ± 5.14 years and the use of other immunosuppressive agents occurred with a mean time of 5.60 ± 3.59 years. Menstrual alterations occurred in 37.9% and amenorrhea in 11.5%. There was an association between menstrual alterations with the use of ISA (P = 0.034). Conclusion: The frequency of menstrual alterations was higher than that found in the general population, similar to what was observed in other publications on lupus treatment. The higher frequency of menstrual alterations in these patients was significantly associated with the use of ISA. The results justify caution when prescribing these medications, research indication and the use of techniques for ovarian preservation means.