Previous measurements of stable isotope ratios in fishes have typically used white muscle, but potential applications exist for the use of other tissues. We tested three tissues (liver, fin, and gonad) in three freshwater species (juvenile Atlantic salmon Salmo salar, slimy sculpin Cottus cognatus, and brook trout Salvelinus fontinalis) to investigate potential ecological applications of stable isotopes in tissues other than muscle. Caudal fin tissue correlated closely with muscle tissue for Atlantic salmon and brook trout for d13C (r = 0.96 and 0.94, respectively) and d15N (r = 0.80 and 0.74). Liver d13C values were tightly linked to muscle values, and differences were due to lipid effects. Associations between liver and muscle d15N suggested subtle changes in nutritional status. Isotope ratios of gonads differed markedly between male and female slimy sculpin; these differences were probably governed by differences in the allocation of specific nutrients. Knowledge of isotopic fractionation among tissues will aid fish biologists in nonlethal sampling of fishes for stable isotope analysis and in using stable isotopes to assess nutritional status and the allocation of nutrients to reproduction.