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BACKGROUND: Optimal treatment of the diseased long head of the biceps (LHB) tendon during rotator cuff repair remains a topic of debate: tenotomy or tenodesis. A recent meta analysis revealed no difference in strength or functional outcome between treatments. The included studies varied in methodological quality, and only two were randomized controlled trials (RCTs). As strong evidence in favor of either tenotomy or tenodesis is still lacking, we designed this randomized controlled trial to compare functional outcomes after tenotomy and tenodesis when performed in adjunct to arthroscopic rotator cuff repair. METHODS: Patients older than 50 years with a supraspinatus and/or infraspinatus tendon rupture sized smaller than 3 cm, who are encountered with LHB pathology, will be randomized to either LHB tenotomy or LHB tenodesis. Clinical and patient-reported data will be collected pre-operatively, 6 weeks, 3 months and 1 year after surgery. Primary outcome is overall shoulder function evaluated with the Constant score at 1 year after surgery. As additional measures of shoulder function, two patient reported outcomes (the Dutch Oxford Shoulder Test and the Disabilities of the Arm Shoulder and Hand questionnaire) will be assessed. Other evaluations include cosmetic appearance evaluated by the "Popeye" deformity, elbow flexion strength, arm cramping pain, MRI-based location of the biceps tendon, quality of life, and duration of surgery. To detect non-inferiority with a one-sided, two-sample t-test with 80 % power and a significance level (alpha) of 0.025, the required sample size is 98 patients. DISCUSSION: Treatment of LHB tendon lesions is performed differently around the world and meta analyses do not provide conclusive evidence in favor of one of these treatments. This study will strengthen evidence on the risks and benefits of LHB tenotomy and tenodesis in adjunct to a rotator cuff repair, which is important for managing patient expectations. TRIAL REGISTRATION: Dutch Trial Register ( NTR3255 ) January 12, 2012, ClinicalTrials.gov (ID NCT02655848 ) January 14, 2016, retrospectively registered.