Parasites can affect host phenotypes, influencing their ecology and evolution. Host morphological changes occurring post-infection might result from pathological by-products of infection, or represent adaptations of hosts or parasites. We investigated the morphology of three-spined sticklebacks, Gasterosteus aculeatus, from a population naturally infected with Schistocephalus solidus, which grows to large sizes in their body cavity. We examined local effects of infection on trunk shape, which are imposed directly by the bulk of the growing parasite, and distant effects on head morphology. We show that trunk shape differed between infection classes, and was affected more severely in fish with heavier total parasite mass. We further show unexpected differences in head morphology. The heads of infected fish were reduced in size and differently shaped to those of non-infected fish, with infected fish having deeper heads. Importantly, both head size and shape were also affected more severely in fish with heavier total parasite mass. This latter result suggests that differences in morphology are caused by post-infection changes. Such changes may be incidental, evolutionarily neutral 'side effects' of infection. However, because head morphology affects foraging ecology, such changes are likely to have fitness consequences for hosts, and may constitute adaptations, either of hosts or of parasites. We discuss our finding in the context of the evolution of phenotypic plasticity, and suggest testable hypotheses examining the proximate mechanisms underlying these morphological effects and their potential evolutionary basis.