Dr. Schaeffer has been Professor and Chairman of the Department of Urology at Northwestern University since 1990. He is best known for his pioneering work in basic and clinical research on urinary tract infections and prostatitis which involves novel concepts for the cause and treatment of these conditions. He has also made major contributions to management of post-prostatectomy incontinence through implementation of a bulbo-urethral sling procedure.

Along with colleagues, he was the first to describe the systemic changes in the mucosal adhesive characteristics that increase the ability of pathogenic bacteria to bind to the mucosa and subsequently cause urinary tract infections in women; to develop a self-start technique for patient-based management of urinary tract infections; to demonstrate that pathogenic bacteria modify expression of their adhesive characteristics in vitro and in vivo; and to determine that an immunoglobulin (secretory IgA) present in vaginal fluid modifies susceptibility to urinary tract infections. For these and other accomplishments he was awarded a National Institutes of Health Merit Award Grant to continue research on urinary tract infections.

He is currently Chair of the National Institutes of Health Multi-Site Collaborative Research Project on male chronic pelvic pain syndrome (prostatitis) and contributes regularly to international panels to establish guidelines for management of urinary tract infections.