Male-killing bacteria are maternally inherited endosymbionts that selectively kill male offspring of their arthropod hosts. Using both analytical techniques and computer simulations, we studied the impact of these bacteria on the population genetics of their hosts. In particular, we derived and corroborated formulas for the fixation probability of mutant alleles, mean times to fixation and fixation or extinction, and heterozygosity for varying male-killer prevalence. Our results demonstrate that infections with male-killing bacteria impede the spread of beneficial alleles, facilitate the spread of deleterious alleles, and reduce genetic variation. The reason for this lies in the strongly reduced fitness of infected females combined with no or very limited gene flow from infected females to uninfected individuals. These two properties of malekiller-infected populations reduce the population size relevant for the initial emergence and spread of mutations. In contrast, use of Wright's equation relating sex ratio to effective population size produces misleading predictions. We discuss the relationship to the similar effect of background selection, the impact of other sex-ratio-distorting endosymbionts, and how our results affect the interpretation of empirical data on genetic variation in male-killer-infected populations. . To our knowledge, there is only one study on the impact of male-killing bacteria on the population genetics of nuclear genes (Telschow et al. 2006). In this theoretical investigation, the process of host adaptation was analyzed in a two-island model, and it was demonstrated that adaptation can be impeded when one population is infected with male-killing bacteria and the other is not infected.Here, we investigate the interplay between selection and drift acting on nuclear alleles in populations infected with male-killing bacteria. We present both analytic approximations and simulation results on the probability of fixation of mutant alleles, the rate of evolution, and expected times until fixation or extinction of alleles. We demonstrate that with respect to these quantities, a male-killer-infected population behaves approximately as it would if it consisted of uninfected individuals only. This means, for example, that the probability of fixation of deleterious alleles is increased in infected compared to uninfected populations, while beneficial alleles have a lower chance of fixation in infected populations. This effect is not due to the distorted population sex ratio, but stems from the peculiar inheritance pattern of nuclear alleles in male-killerinfected populations, in which gene flow from infected to uninfected individuals is constrained. The effects are observed even when the male-killer is inefficiently transmitted.