The study investigated the effects of a temperature shift during embryogenesis on diploid and triploid Atlantic salmon (Salmo salar L.) embryo development and juvenile skeletal deformities. From fertilization, sibling populations were incubated under one of three temperatures (6, 8 or 11°C) until 400 °days when all fish were then reared under a common temperature until smolt. Survival was negatively impacted by increasing temperatures irrespective of ploidy. There was no effect of incubation temperatures on growth in diploids, but triploids incubated at 6°C had improved growth rates (thermal growth coefficient, TGC: 6°C: 1.05, 8°C: 0.94, 11°C: 0.48). Fish from 11°C in both ploidies showed increased jaw and vertebral deformity prevalence. In response to the temperature change at 400 °days post fertilization, upregulation of bmp2, bmp4, col2a1, mmp13, opn and sparc, and downregulation of ocn further suggest that bone and cartilage formation is compromised after experiencing a thermal shift. The data show that temperature profile during embryogenesis strongly influences future growth and deformity prevalence. Triploids appear to require a lower incubation temperature than the current industry standard of 8°C to promote better overall performance; however, a thermal shift during embryogenesis was shown to impact expression of important developmental genes.