Background: During rotator cuff repair, biceps tendon lesions are frequently encountered. However, there is still controversy about optimal treatment for these lesions. Purpose: To compare the results of tenotomy and suture anchor tenodesis prospectively. Study Design: Cohort study; Level of evidence, 2. Methods: From January 2006 to June 2007, 90 patients (age, >55 years) with a rotator cuff tear and biceps tendon lesion (tear more than 30%, subluxation or dislocation, or degenerative superior labrum anterior to posterior lesion type II) were evaluated prospectively. The first 45 patients treated consecutively underwent biceps tenodesis, and the next 45 underwent biceps tenotomy. Postoperatively, patient evaluations were conducted with a focus on (1) “Popeye” deformity, (2) arm cramping pain, and (3) elbow flexion powers (measured with a hand dynamometer). Overall shoulder function was assessed with the American Shoulder and Elbow Surgeons (ASES) score and the Constant score. Results: At final follow-up, 43 in the tenodesis and 41 in the tenotomy groups were available for evaluation. There was no difference between groups in demographic data such as age, sex, dominant arm, and the time from symptom to surgery and in preoperative ASES score, Constant score, and rotator cuff tear size. A Popeye deformity occurred in 4 (9%) in the tenodesis group and in 11 (27%) in the tenotomy group (P = .0360). Mild cramping pain was observed in 2 in the tenodesis group and 4 in the tenotomy group (P = .4274). Mean elbow flexor power ratio (vs the contralateral side) showed no difference between the 2 groups, with mean values of 0.92 ± 0.15 (tenodesis) and 0.94 ± 0.19 (tenotomy) (P = .7475). The ASES and Constant scores were improved from 38.9 ± 14.2 and 52.1 ± 21.3 to 84.7 ± 13.6 and 82.9 ± 13.5 in the tenodesis group (P < .0001) and from 35.2 ± 10.5 and 48.1 ± 21.3 to 79.6 ± 15.8 and 78.3 ± 14.1 in the tenotomy group (P < .0001), respectively. Conclusion: Suture anchor tenodesis of the long head of the biceps tendon appears to lead to less Popeye deformity than tenotomy. No other clinical variables showed a difference between the 2 modalities.