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Lung Cancer is the most common cause of cancer-related death worldwide. Early and automatic diagnosis of Solitary Pulmonary Nodules (SPN) in Computer Tomography (CT) chest scans can provide early treatment as well as doctor liberation from time-consuming procedures. Deep Learning has been proven as a popular and influential method in many medical imaging diagnosis areas. In this study, we consider the problem of diagnostic classification between benign and malignant lung nodules in CT images derived from a PET/CT scanner. More specifically, we intend to develop experimental Convolutional Neural Network (CNN) architectures and conduct experiments, by tuning their parameters, to investigate their behavior, and to define the optimal setup for the accurate classification. For the experiments, we utilize PET/CT images obtained from the Laboratory of Nuclear Medicine of the University of Patras, and the publically available database called Lung Image Database Consortium Image Collection (LIDC-IDRI). Furthermore, we apply simple data augmentation to generate new instances and to inspect the performance of the developed networks. Classification accuracy of 91% and 93% on the PET/CT dataset and on a selection of nodule images form the LIDC-IDRI dataset, is achieved accordingly. The results demonstrate that CNNs are a trustworth method for nodule classification. Also, the experiment confirms that data augmentation enhances the robustness of the CNNs.