Cigarette smoking is a lifestyle behaviour associated with significant adverse health effects including subfertility and premature ovarian failure. Cigarette smoke contains a number of Aryl hydrocarbon receptor agonists, the activation of which leads to induction of cytochrome P450, which is involved in the generation of reactive oxygen species (ROS). Oxidative stress and the production of ROS can lead to both apoptosis and autophagy. Autophagy is a fundamental cellular process that removes long-lived proteins and damaged organelles through lysosomal degradation. The relevance of autophagy to granulosa cell death and toxicant-induced changes in ovarian function are largely unexplored. Recently, our lab reported that exposure to cigarette smoke causes significant primordial follicle loss, a decrease in the cell's ability to cope with the production of reactive oxygen species and the activation of the autophagy pathway as evidenced by the presence of autophagolysosomes in treated ovaries, a decrease in the expression of SOD2 and the increased gene expression of Beclin-1 and LC3. The changes in SOD2 expression points to changes in mitochondrial function. Mitochondria are essential organelles that power the cell and exist in a dynamic interconnected network that is constantly reshaped by a balance between fission and fusion. This balance is tightly regulated to maintain appropriate mitochondrial content in daughter cells and allow repair of damaged mitochondria. Disruption of mitochondrial dynamics and inhibition of mitochondrial fusion has been implicated in a number of neurodegenerative diseases including Parkinson's and Alzheimer's. To date, however, mitochondrial dynamics have not been investigated in the granulosa cells of smokers. Therefore, the present study was designed to test the hypothesis that cigarette smoke exposure results in the dysregulation of the mitochondrial repair mechanism leading to the loss of follicles via autophagy-mediated granulosa cell death. In this study, mice were exposed to cigarette smoke or room air (control) for 8 weeks. Ovaries were excised and processed for histology, Western blotting, immunohistochemistry and quantitative real time-PCR. Decreased SOD2 expression (p < 0.001) and that of two mitochondrial pro-fusion proteins, mitofusin-1 (MFN1, p = 0.003) and MFN2 (p = 0.02), coupled with the increased expression of a pro-fission protein, Parkin (p = 0.006), suggests that cigarette smoke exposure triggers mitochondrial damage in cigarette smoke exposed ovaries. Moreover, the autophagy cascade protein, LC3, was significantly up-regulated (p = 0.032), while Bcl-2, an inhibitor of autophagy, was down-regulated (p = 0.003) following cigarette smoke exposure. Taken together, our results suggest that cigarette smoke exposure causes mitochondrial repair mechanisms to dysfunction, leading to autophagy-mediated follicle death.