The use of low-dose Computer Tomography (CT) has been effective in reducing the mortality rate of lung cancer. With the rapid increase in the number of studies, computer aided diagnosis (CAD) systems need to be developed to further assist radiologists in detecting and classifying lung nodules in CT scans. In this paper we propose a new system based on Deep Convolutional Neural Networks, U-net, and ResNet architectures. This network performs the dual task of registration of lung nodule scans in two time points and additionally performs benign/malignant classification. The training and testing data were put together based on a subset of data from the National Lung Screening Trial (NLST), referred to as NLSTx which has biopsy confirmed diagnoses for the nodules. The combination of deformable registration and binary classification performed by the network will increase the usefulness of this CADx system allowing both measurement of the growth and classification of the nodule.