Dyspareunia and vaginismus are complex disorders involving a myriad of predisposing, precipitating and perpetuating factors that make painful intercourse a difficult symptom to relieve. A multidisciplinary, intersystems approach to etiology, assessment, and treatment is proposed as the optimal standard of care, with the collaboration of sex therapy, gynecology, and physical therapy. Etiology is reviewed as potentially involving physiological, psychological, couple, intergenerational, and sociocultural causes and influences. It is recommended that initial assessment focus on the properties of the pain, sexual function, and individual cognitive and coping styles. The assessment of relational, intergenerational, and sociocultural factors is best integrated throughout treatment. It is also recommended that treatment commence with education, goal setting, and anxiety reduction to then proceed to the systematic targeting of pain and physiological processes, sexual interactions, individual schema, and relationship dynamics. The challenges of treatment are identified as primarily consisting of multidisciplinary coordination, the tension between structure and spontaneity, the management of expectations, and definitions of treatment success. Finally, an appeal is made for future research to take a systems approach to the study of dyspareunia and vaginismus, as well as to increase the diversity of populations studied.