Wolbachiais a common endosymbiont that can protect insects against viral pathogens. However, whether the antiviral effects ofWolbachiahave a significant effect on fitness remains unclear. We have investigated the interaction betweenDrosophila melanogaster, Wolbachiaand two viruses that we recently isolated from wild flies, La Jolla virus (LJV;Iflaviridae) and Newfield virus (NFV;Permutotetraviridae). Flies infected with these viruses have increased mortality rates, and NFV partially sterilizes females. These effects on fitness were reduced inWolbachia-infected flies, and this was associated with reduced viral titres. However,Wolbachiaalone also reduces survival, and under our experimental conditions these costs of the symbiont can outweigh the benefits of antiviral protection. In contrast, protection against the sterilizing effect of NFV leads to a net benefit ofWolbachiainfection after exposure to the virus. These results support the hypothesis thatWolbachiais an important defense against the natural pathogens ofD. melanogaster.Furthermore, by reducing the cost ofWolbachiainfection, the antiviral effects ofWolbachiamay aid its invasion into populations and help explain why it is so common in nature.