ABSTRACT Effective population size ( N e ) is a key parameter for understanding evolutionary processes, but it is generally not considered in epidemiological studies or in studying infections of individual hosts. Whether N e has an effect on the onset of symptoms and viral accumulation in Tobacco etch virus (TEV) infection of Nicotiana tabacum plants is considered here. Using mixtures of TEV variants carrying fluorescent markers, the dose dependence of N e was confirmed, and the inoculation procedure was found to be the main source of variation in these experiments. Whereas the onset of symptoms was independent of N e , there was less and more variable accumulation at 6 days postinoculation for small N e values ( N e < 5). The observed variation in accumulation was not heritable, however, suggesting that this variation was not due to the fixation of deleterious mutations in the small founder populations. On the other hand, virus-induced fluorescence and accumulation in the inoculated leaf were strongly N e dependent. Systemic accumulation was independent of N e , although removal of the inoculated leaf led to a small reduction in systemic accumulation for small N e values. For whole plants, N e -dependent effects on accumulation were no longer observed at 9 days postinoculation. Therefore, the effects of N e on accumulation are due mainly to limited expansion in the inoculated leaf and are transient. In this system, N e -dependent effects will be strongest at low doses and early in infection. We conclude that N e can have implications for epidemiology and infection at the individual host level, beyond determining the rate of mixed-genotype infection.