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Objective Sexual functioning is an important component of life quality and musculoskeletal disorders may effect sexual functioning, so, the present study was conducted to evaluate sexual functioning in patients suffering from back pain, rheumatoid arthritis, and systemic lupus erythematosus (SLE). Methods This study was conducted on 102 patients with rheumatoid arthritis, 103 patients with back pain, 103 patients with SLE, and 210 people in the control group by the consecutive sampling method. The marital satisfaction questionnaire (Enrich), Arizona Sexual Experience Scale (ASEX) questionnaire, and the General Health Questionnaire (GHQ‐28) were completed by all the subjects. Disease severity was determined in each group of patients by Disease Activity Score of 28 joints, the Roland Morris questionnaire, and the SLE Disease Activity Index questionnaire. Results The GHQ in rheumatoid arthritis and lupus patients was meaningfully higher than the control group (P < .05), while there was no meaningful difference between back pain patients and the control group (P = .414). The sexual functioning questionnaire score in all 3 groups showed no statistically meaningful difference with the control group (P < .05). Also, the marital satisfaction questionnaire score in all the groups showed no statistically meaningful difference compared to the control group (P = .791). Conclusion The study has shown that the level of sexual function in participants with back pain and the level of mental health and sexual functioning in patients with rheumatoid arthritis and SLE are significantly lower than healthy people and there is a need for intervention for improving mental health as well as sexual functioning in these patients.