From 2004 to 2008 we evaluated 431 SLAP lesions during 3,395 shoulder arthroscopies and compared two groups of patients, one with SLAP lesion as group I and one without SLAP lesions as group II. Exclusion of type I SLAP lesions, rotator cuff tears and history of dislocation of the shoulder in both groups left 182 cases in group I, and additionally, exclusion of all-type SLAP lesions left 251 patients in group II. In group I, SLAP lesion-associated chondral lesions were present in 20% at the humerus (4% group II, p = 0.005), 18% at the glenoid (5% in group II, p = 0.05) and 14% glenohumeral (3% group II, p = 0.04). We observed a pattern of typical localization of SLAP-associated chondral lesions at the humerus underneath the biceps tendon (78%) and at the anterior half of the glenoid (63%) in group I in contrast to the central region of the humerus (82%) and the central region at the glenoid (55%) in group II. The association of SLAP and chondral lesions was not influenced by the presence of trauma or age of the patients. SLAP lesions seem to be a risk factor for subsequent early onset of osteoarthritis either caused by a bicipital chondral print or glenohumeral instability or a combination of both.