Introduction: This study assessed the agreement of cone-beam computed tomography (CBCT) scan and sinus endoscopy findings and attempted to find a diagnostic accuracy of CBCT in patients with chronic rhinosinusitis (CRS). Methods: Forty-two patients with CRS referred to the Aria and 22 Bahman Hospitals in Mashhad, Iran, during the year 2011 were included in this cross-sectional study. Paranasal sinus CBCT scanning and endoscopy were performed in all patients. The sensitivity, specificity, positive and negative predictive values (PPV and NPV), and accuracy of CBCT were determined, and the agreement between CBCT and endoscopy findings was evaluated. Results: In most of our findings, except for infundibulum thickening, there was a strong agreement between CBCT and paranasal sinus endoscopy, with a kappa coefficient >0.80 (p < 0.05). The sensitivity, specificity, PPV, NPV, and accuracy of CBCT were >80% for most of the findings, except for infundibulum thickening and septal deviation. Conclusion: CBCT has nearly the same diagnostic accuracy as sinus endoscopy. The accuracy of CBCT scanning is high, and CBCT findings are well correlated with sinus endoscopy findings. Considering its high accuracy and lower costs and radiation doses, CBCT may be a proper alternative method for diagnostic sinus endoscopy in the assessment of CRS in patients with a contraindication for sinus endoscopy.