Zygapophysial joint (z-joint) pain has long been suggested to be one of the sources of low back pain. Radiofrequency denervation of the medial branches of the dorsal rami to treat z-joint pain is an outpatient minimally invasive treatment option. There have been many short-term studies to determine the outcome of the procedure, but few long-term studies have been conducted. Our goal is to clarify whether radiofrequency denervation has any long-term clinical benefit. In this retrospective cohort study, a total of 42 patients (25 women and 17 men), with an average follow-up of 3.5 years, with clinical signs of zygapophysial joint involvement who had failed conservative treatment (pre-procedure symptom duration mean 6.03 years; range 5 months to 48 years) and had a favorable response to a diagnostic medial branch block or zygapophysial joint injection, were identified. The identified subjects underwent radiofrequency denervation at the Hospital for Special Surgery Physiatry Department from 1998 to 2006. Patient's records were reviewed, and a questionnaire was provided, completed on phone call follow-up, or mailed by the patient. The success of this intervention in providing improvement in pain and function was analyzed using the Numerical Rating Scale (NRS)-11, North American Spine Society (NASS) four-point satisfaction index, and a modified Roland-Morris Disability Questionnaire (RMDQ). Fifty-two percent of patients reported a successful outcome with improved function at a minimum follow-up period of 2 years (mean 3.5 years, range 2-8.8 years). Patients in the failure group were more likely to be older and have moderate to severe neuroforaminal stenosis (77.8%) compared to patients in the success group (24.2%). Radiofrequency denervation in selected patients with chronic zygapophysial joint-mediated low back pain provides long-term reduction in pain and improved function with minimum morbidity.