The population-level dynamics of maternally transmitted endosymbionts, including reproductive parasites, depends primarily on the fitness effects and transmission fidelity of these infections. Although experimental laboratory studies have shown that within-host endosymbiont density can affect both of these factors, the existence of such effects in natural populations has not yet been documented. Using quantitative PCR, we survey the density of male-killing Wolbachia in natural populations of Drosophila innubila females from the Chiricahua Mountains of Arizona. We find that there is substantial (20 000-fold) variation in Wolbachia density among wild flies and that within-host Wolbachia density is positively correlated with both the efficacy of male killing and maternal transmission fidelity. Mean Wolbachia density increases three- to five-fold from early to late in the season. This pattern suggests that Wolbachia density declines with fly age, a conclusion corroborated by a laboratory study of Wolbachia density as a function of age. Finally, we suggest three alternative hypotheses to account for the approximately lognormal distribution of Wolbachia density among wild flies.