The percutaneous muscle biopsy technique is an important tool used in exercise and applied physiology to study human skeletal muscle structure, adaptation, and regeneration. One important use of this technique has been the assessment of ultrastructural muscle damage, especially in tissue samples obtained following strenuous exercise protocols, often involving eccentric muscle actions. In this brief review, we define and describe hypercontracted fibers, and outline how such fibers may adversely affect the interpretation of muscle damage from fixed tissue. Evidence suggests that hypercontracted fibers present in healthy skeletal muscle samples are likely to be artifacts related to the muscle biopsy procedure, as opposed to intrinsic degeneration present prior to the biopsy. When hypercontracted fibers are noted as being intrinsic to a muscle sample (e.g., in myopathy or following an extreme eccentric stimulus), such fibers are generally associated with the infiltration of inflammatory cells, indicative of a regenerative response. In contrast, hypercontracted fibers resulting from the biopsy procedure are not typically associated with an inflammatory response. The major sources of hypercontracted fibers are outlined and recommendations for their interpretation are discussed.