The aim of the present study was to examine the effects of tetraploidy induction on proteome of rainbow trout during the early stages of development. After insemination, the eggs were incubated at 10 °C for 350 min. Thereafter, half of the eggs were exposed to a heat-shock of 28 °C for 10 min. The remainder were incubated normally and used as diploid controls. Fertilized egg specimens were selected 390 min post-fertilization. Samples corresponding respectively to eyed embryos and fry stages were also taken on days 18 and 76 post-fertilization. Based on two-dimensional electrophoresis, all spots that were found to differ significantly in abundance between the untreated and heat-shock treated groups were selected for identification using MALDI-TOF/TOF mass spectrometry. Out of 19 protein spots showing altered abundance in the present study, 13 spots were successfully identified. Of the spots that were shown to change in abundance in the fertilized eggs with heat-shock treatment, three were identified as vitellogenin (spots 1, 2 and 3); while the others were creatine kinase (spot 5) and nucleoside diphosphate kinase (spot 6). All of the proteins identified in the embryos were related to vitellogenin (spots 8, 12 and 13). Among the identified spots from the fry muscle extracts, two were identified as beta-globin (spots 14 and 17); while the others were parvalbumin (spots 15 and 16) and creatine kinase (spot 19). The results obtained in our study may now set the ground for investigations on gene regulation and proteome modifications in polyploid fish.