Rotator cuff tears are a major cause of morbidity. Following rotator cuff tears, muscle atrophy and fatty infiltration begin in the tissue, limiting repair potential and leading to a higher re-tear rate and a worse functional outcome. We evaluated whether fatty degeneration resulting from a complete supraspinatus tear with retraction is associated with an injury to the suprascapular nerve. Four skeletally mature New Zealand white rabbits were randomized to receive an index procedure on either their right or left shoulder with the opposite shoulder serving as a control. At the index procedure, the supraspinatus tendon was transected at its insertion and allowed to retract. At 3 months, the rabbits were euthanized, and both supraspinatus muscles were harvested. The specimens were then examined with confocal microscopy and histology. Atrophy was grossly visible in all four test muscles, and fatty infiltration was confirmed with osmium tetroxide staining. In all four rabbits, the degree of denervation (p = 0.71) and partial denervation (p = 0.91) was not significantly different between control and experimental muscle. Rotator cuff tear does not affect the motor endplate or innervation status of the supraspinatus. Fatty infiltration occurs independent of denervation of the supraspinatus. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:99–104, 2012