The aim of this study was to investigate the effects of vaccination, and starvation after vaccination, on the morphology of skull bones and vertebral bodies, bone mineralization and the development of intra-muscular melanin deposits in farmed Atlantic salmon. For this purpose, triplicate groups of vaccinated (V) or unvaccinated (UV) underyearling smolts (38 g) were fed normal rations (F), or starved for 3 weeks after vaccination (S) (September 2004), leaving four experimental groups (V-F, V-S, UV-F, UV-S). After termination of the starvation period, all groups were fed a normal ration until the fish reached a normal harvest size (January 2006). There were no long term effects of starvation on body weight, bone mineralization or deformity incidence. However, at termination, V fish (pooled mean V-F and V-S, 4.4 kg) were overall significantly smaller than UV fish (pooled mean UV-F and UV-S, 5.1 kg), and they also developed overall significantly more deformities in both the skull (pooled mean UV-F and UV-S 27%, pooled mean V-F and V-S 81%) and the vertebral column (pooled mean UV-F and UV-S 21%, pooled mean V-F and V-S 41%). These deformities were site-specific in both compartments; skull deformities were clearly observed in the ceratohyale anterior, while those in the vertebral column were mainly located in the tail region (V31–49). There were no significant correlations among individual relationships between the skull and vertebral column deformities. UV fish had overall significantly higher vertebral bone total ash content than V fish at termination, but there were no effects on vaccination on the ash content or morphology of the vertebrae 2 months after transfer to seawater. The incidences of intra-muscular melanin deposits were not significantly different between UV and V fish. These results show that vaccination can induce deformities in the vertebral column and/or skull in farmed Atlantic salmon. The site-specific location of the deformities in relation to mechanical loading is discussed. Furthermore, the results show that vaccination is not likely the main cause of the current melanin spot problem in Atlantic salmon aquaculture.