Background The literature directly comparing the utility of clinical examination (CE) to that of CT in detecting recurrence of squamous cell carcinoma (SCC) for primary site recurrences is lacking. Methods Patients who received both CT scans and CEs after primary treatment for SCC of the upper aerodigestive tract (oropharynx, hypopharynx, and larynx) were identified. Individual CT scans and CEs were evaluated for their ability to detect recurrence status. Results One hundred thirty-one patients underwent a total of 886 CEs and 346 CT scans during the follow-up period. The sensitivity for CE and CT was 84.0% and 66.7%, respectively; for specificity, 98.7% and 90.7%, respectively; for positive predictive value, 65.6% and 31.8%, respectively; and for negative predictive value the values were 99.5% and 97.7%, respectively. Conclusion Due to the low sensitivity and positive predictive value of CT scans compared to physical examination in evaluating primary site tumor recurrences, the utility of CT for surveillance may be limited. Copyright © 2010 Wiley Periodicals, Inc.