The aggregation of abnormally folded proteins is a defining feature of neurodegenerative disease, but it has not previously been possible to assess the conformation of these proteins in a physiologically relevant context, before they form morphologically recognizable aggregates. We now describe FRET-based reporters for the conformation of alpha-synuclein, a protein central to the pathogenesis of Parkinson's disease (PD). Characterization in vitro shows that alpha-synuclein adopts a relatively "closed" conformation in solution that converts to "open" on membrane binding. In living cells, the closed conformation predominates. In neurons, however, cell bodies contain a much larger proportion of the open conformation than synaptic boutons. To account for these differences, we also used the reporters to characterize the interaction with native membranes. We find that the conformation of alpha-synuclein responds selectively to mitochondria, indicating a direct link between alpha-synuclein and an organelle strongly implicated in the pathogenesis of PD.