The fresh-water crustacean Daphnia magna may acquire an infection with the microsporidium Octosporea bayeri either by ingesting spores from the water (horizontally), or directly from its mother (vertically). Due to differences in the time and mechanisms of transmission, horizontal and vertical infections may lead to differences in the growth of the parasite within the host. This may influence parasite virulence, transmission to new hosts, and, consequently, epidemiology and evolution. Here we describe the within-host dynamics of 3 spore-types of O.bayeri from infections that were acquired either horizontally or vertically. In all treatments the number of spores increased exponentially until spore density reached a plateau, suggesting density-dependent within-host growth. The spore types seen differ in their growth dynamics, suggesting different roles in the parasite life-cycle. Horizontally-infected hosts harboured significantly fewer spores than vertically-infected hosts. Further, host survival was affected by infection route, with mortality being higher in horizontal infections than in vertical infections. Our results suggest that different routes of infection have an immediate effect on within-host parasite growth and thus on parasite fitness and epidemiology.