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Temperature stress on developing steelhead (Oncorhynchus mykiss) was evaluated using asymmetry of skeletal characters, fish condition factor, and metabolic fingerprints. Eggs from three female hatchery steelhead were fertilized by a single male. The eggs from each female were divided into two groups and incubated at either 8°C or 18°C. Mortality, growth, and condition factor were measured at stage 6 (32 cells), stage 20 (eyed), and stage 21 (caudal flexing). In addition, 1H-nuclear magnetic resonance (NMR) spectroscopy was used to establish metabolic fingerprints of developing eggs at the three stages. After hatching, all alevins were moved to tanks at 18°C and allowed to develop to 60 days post-emergence (DPE), at which point they were examined for structural asymmetry. Eggs incubated at 18°C experienced higher mortality, with all eggs from one hen dying at the higher temperature. Eggs incubated at the higher temperature that did survive hatched as larger larval fish than eggs incubated at the lower temperature. Fish incubated at the higher temperature exhibited greater structural asymmetry than fish incubated at the lower temperature. A principle components (PC) analysis of the metabolic fingerprints indicated that PC1 and PC2 accounted for 60% of the variance in the metabolites. Separation along PC1 corresponded to differences in developmental stage, and separation along PC2 corresponded to differences in hen. Eggs incubated at 18°C lagged behind eggs incubated at 8°C along PC1, indicating a potential problem with embryo staging. PC1 scores were highly correlated with the accumulated thermal units during development, indicating that scores along PC1 were a robust measure of developmental stage.