A proteomic screening approach was employed to achieve a better understanding of the changes that occur in protein expression patterns associated with skeletal deformities in both diploid and triploid rainbow trout larvae. Triploidy was induced through the application of heat shock of 28 °C for 10 min to eggs 10-min post fertilization in an aquarium equipped with a heater. Percentage of skeletal deformity in heat-shocked larvae (2.88 ± 0.30, mean ± S.E.) was significantly (P < 0.05) greater than that of the diploids (0.55 ± 0.24). At five days after hatching, proteins of normal and deformed specimens of deyolked larvae were subjected to proteomic analysis using two-dimensional electrophoresis and mass spectrometry. Among the identified protein spots from diploids, creatine kinase was found to be increased in larvae with skeletal deformities, while apolipoprotein A-I-2, apolipoprotein A-II and calmodulin were found to be decreased in deformed fish. Among the five protein spots that were identified in heat-shocked fish, apolipoprotein A-I-2, apolipoprotein A-II, parvalbumin, myosin light chain 1-1 and nucleoside diphosphate kinase were found to be decreased in deformed larvae. The identification of nine protein spots showing altered expression in deformed fish allows us to reach a preliminary view of the molecular mechanisms that are involved in the development of skeletal malformations in diploid and triploid fish.