This study compared the sexual and relationship functioning of 38 male patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) to that of their female partners, and of both the men and women in these couples to those in 37 control couples. Male sexual function was also examined as a predictor of partner sexual function. In comparison to control males, the men with CP/CPPS reported significantly more sexual dysfunction and symptoms of depression. Furthermore, symptoms of depression mediated the relationship between some aspects of sexual function and male participant status as a patient or control. However, men with CP/CPPS did not report significantly decreased sexual satisfaction or relationship functioning compared to controls. Partners of men with CP/CPPS reported significantly more pain upon intercourse, vaginismus, and depressive symptoms when compared to control females. In addition, patients with CP/CPPS and their partners did not differ significantly from each other with regard to sexual functioning and satisfaction, relationship functioning, and symptoms of depression. Patient sexual functioning significantly predicted female partner sexual functioning. This study was the first to evaluate partners of men with CP/CPPS. Patients and partners in this study reported lower levels of sexual functioning in some domains, yet were comparable to control couples on measures of satisfaction and relationship functioning. Furthermore, the sexual and relationship functioning of patients and partners was significantly associated. The results of this study have implications for the assessment and management of CP/CPPS and for future research in this area.