INTRODUCTION: Nonsteroidal anti-inflammatory drugs (NSAIDs) have a well-established analgesic efficacy for inflammatory pain. These drugs exert their effect by inhibiting the enzyme cyclooxygenase (COX) and are commonly used for the management of pain after endodontic treatment. There are 2 distinct isoforms of COX: COX-1, which is constitutively expressed, and COX-2, which is primarily induced by inflammation. Previous studies have shown that functional human genetic variants of the COX-2 gene may explain individual variations in acute pain. The present study extends this work by examining the potential contribution of the 2 COX isoforms to pain after endodontic treatment. METHODS: Ninety-four patients treated by endodontic residents at the University of North Carolina School of Dentistry were enrolled into a prospective cohort study. Data on potential predictors of post-treatment pain were collected, and all patients submitted saliva samples for genetic analysis. Nonsurgical root canal therapy was performed, and participants recorded pain levels for 5 days after. RESULTS: In this study, 63% of patients experienced at least mild pain after root canal therapy, and 24% experienced moderate to severe pain. The presence of pretreatment pain was correlated with higher post-treatment pain (P = .01). Elevated heart rate (P = .02) and higher diastolic blood pressure (P = .024) were also correlated with decreased post-treatment pain. Finally, we identified genetic variants in COX-2 (haplotype composed of rs2383515 G, rs5277 G, rs5275 T, and rs2206593 A) associated with post-treatment pain after endodontic treatment (P = .025). CONCLUSIONS: Understanding the genetic basis of pain after endodontic treatment will advance its prevention and management.