Peripheral artery disease (PAD), characterized by blockages of the arteries to the legs, affects approximately 8 million lives in the United States. This injury includes altered metabolic processes, damaged organelles, and compromised bioenergetics in the affected muscle. In this study, we evaluated the hypothesis that Fourier Transform Infrared (FTIR) spectroscopy of human biopsy samples (gastrocnemius muscle) can be used to identify biochemical alterations in PAD muscle and characterize severity of muscle damage. When comparing spectral peaks between controls and patients with PAD, significant differences were found in the fingerprint region. FTIR spectroscopy was able to characterized the secondary effect of PAD on the gastrocnemius by identifying unique biochemical signatures of diseased PAD skeletal muscle.