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Tendinopathy is a vexing clinical problem as its onset and development is often asymptomatic and unrecognized until tendon rupture. While extensively studied in the rotator cuff, Achilles, and patellar tendons, no study to date has examined the histological and molecular characteristics of the tendinopathic biceps long-head (LHB). The anatomy of the LHB is unique in that it comprises intra- and extra-articular portions, each exposed to differing loading patterns. Eleven LHBs post-tenotomy were sectioned, fixed in formalin, and stained (H and E; Alcian Blue), and gross structural organization of collagen measured using polarized light microscopy. Protein expression of intra- and extra-articular portions of the tenotomized biceps for IGF-I, collagen III, and MMP-1, -2, -3, and -13 was determined with Western blot analyses. The intra-articular LHB exhibited significantly greater histological evidence of tendinopathy inclusive of increased proteoglycan (p < 0.05) and decreased organization as measured by polarized light microscopy (p < 0.01). The intra-articular LHB also had significantly increased expression of collagen type III (p < 0.01) and of MMP-1 and 3 (p < 0.01, p < 0.05 respectively). No significant differences were found for IGF-I or for MMP-2 and -13. The intra-articular LHB exhibited histological characteristics of tendinopathy. Protein expression of the intra-articular LHB did not universally display signs of tendinopathy in comparison to the extra-articular portion of the tendon.