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Parkinsonism is the second most common neurodegenerative disease, originated by a dopamine decrease in the striatum. Single Photon Emission Computed Tomography (SPECT) images acquired using the DaTSCAN drug are a widely extended tool in the diagnosis of Parkinson’s Disease (PD), since they can measure the amount of dopamine transporters in the striatum. Many automatic systems have been developed to aid in the diagnosis of PD, using traditional feature extraction methods. In this paper, we propose a novel system based on three-dimensional Convolutional Neural Networks (CNNs), that aims to differenciate between PD-affected patients and unaffected subjects. The proposed system achieves up to a 95.5% accuracy and 96.2% sensitivity in the diagnosis of PD.