Muscles subjected to lengthening contractions (eccentric contractions) exhibit evidence of subcellular disruption, arguably a result of fiber strain magnitude. Due to the difficulty associated with measuring fiber strains during eccentric contractions, fiber length estimates have been used to formulate relationships between the magnitude of injury and mechanical measures such as fiber strain during in-vitro and in-situ experiments. In these protocols, the series compliance is typically minimized by removing the distal tendon and/or pre-activating the muscle. These in-vitro and in-situ experiments do not represent physiologic contractions well where fiber strain and muscle strain may be disassociated, thus the mechanisms of in-vivo muscle injury remain elusive. The purpose of this paper was to quantify fiber strains during lengthening contractions in-vivo, and assess the potential role of fiber strain in muscle injury following repetitive stretch-shortening cycles. Using intact NZW rabbit dorsiflexors, fiber strain and joint torque were measured during 50 active lengthening and passive shortening cycles. We were able to show that fiber length changes are disassociated from MTU length changes for some parts of the stretch-shortening cycle, and that the complex fiber dynamics during these cycles prevent easy estimates of fiber strains from MTU length changes. In addition, fiber strains vary depending on how they are defined, and strains vary from repetition to repetition during the fifty stretch-shortening cycles, thereby further complicating the potential relationship between muscle injury and fiber strain. We conclude from this study that during in-vivo stretchshortening cycles, the relationship between fiber strain and muscle injury is complex. This is due, in part, to the temporal effects of repeated loading on fiber strain magnitude that may be explained by an increasing compliance of the contractile element as exercise progresses.