Dietary patterns of leprosy patients from the medieval leprosarium at Odense (Denmark) were investigated via carbon isotope ratio analysis of individual amino acids (δ13CAA) in bone collagen. The aim of this research was to explore in detail the consumption of aquatic resources (freshwater and marine) by these individuals; especially during the last few years of life, which were likely spent in the leprosy hospital. The analysis was conducted on ribs (n = 30) and long bones (n = 10) from 30 individuals, as well as on 9 local and contemporary faunal samples. A comparison of the Odense δ13CAA results with published δ13CAA values from the Baltic Sea region indicate that the diet was primarily terrestrial, but 12 of the 30 individuals (40%) consumed a mixed terrestrial-aquatic diet based on Δ13CVal-Phe values. Further, comparison of the rib-long bone pairs from 10 individuals found statistically significant differences in the Δ13CVal-Phe and Δ13CGly-Phe results, but not the δ13CLys results. This intra-individual dietary difference is also supported by MLA-PCA, and tentatively suggests these leprosy patients increased their consumption of marine protein over the last few years of life, indicating perhaps an institutional dietary program in the leprosarium. This work represents one of the largest archaeological δ13CAA studies in Europe and the first to compare bones with different turnover rates. Compound specific isotope analysis of δ13CAA has great potential to reveal subtle intra-individual dietary shifts that may remain undetected by bulk isotopic analysis.