In gastropods, variation in shell morphology can be caused by the action of several biotic and abiotic factors. While much of this variation is seen in comparisons between different sites or populations, there is also substantial variation in shell morphology among individuals living side by side. We investigate the effect of trematode parasitism on both intra- as well as inter-site variation in the morphology of the New Zealand whelk Cominella glandiformis. We found that both infection by the trematode Curtuteria australis and site of origin had significant effects on several morphometric dimensions of the snail shell, with some interactions between the two factors. On its own, infection by C. australis accounted for 20 to 60% of the variance in shell morphology, depending on the dimension measured. Infected snails also had smoother shells, with less prominent ridges, than their uninfected conspecifics. Other trematode species, infecting whelks at much lower prevalence, also had impacts on shell morphology, but not necessarily in the same direction as C. australis. Overall, parasitism may be an important factor in explaining intra- and inter-site variation in snail phenotype, with potential repercussions for snail populations and their interactions with other community members.