Introduction: Mitochondrial dysfunction and oxidative stress are critical factors in the pathogenesis of age-dependent neurodegenerative diseases. PGC-1 alpha, a master regulator of mitochondrial biogenesis and cellular antioxidant defense, has emerged as a possible therapeutic target for Parkinson's disease, with important roles in the function and survival of dopaminergic neurons in the substantia nigra. The objective of this study is to determine if the loss of PGC-1 alpha activity contributes to alpha-synuclein-induced degeneration. Results: We explore the vulnerability of PGC-1 alpha null mice to the accumulation of human alpha-synuclein in nigral neurons, and assess the neuroprotective effect of AAV-mediated PGC-1 alpha expression in this experimental model. Using neuronal cultures derived from these mice, mitochondrial respiration and production of reactive oxygen species are assessed in conditions of human alpha-synuclein overexpression. We find ultrastructural evidence for abnormal mitochondria and fragmented endoplasmic reticulum in the nigral dopaminergic neurons of PGC-1 alpha null mice. Furthermore, PGC-1 alpha null nigral neurons are more prone to degenerate following overexpression of human alpha-synuclein, an effect more apparent in male mice. PGC-1 alpha overexpression restores mitochondrial morphology, oxidative stress detoxification and basal respiration, which is consistent with the observed neuroprotection against alpha-synuclein toxicity in male PGC-1 alpha null mice. Conclusions: Altogether, our results highlight an important role for PGC-1 alpha in controlling the mitochondrial function of nigral neurons accumulating alpha-synuclein, which may be critical for gender-dependent vulnerability to Parkinson's disease.