In this study, we propose and validate an end-to-end pipeline based on deep learning for differential diagnosis of emphysema in thoracic CT images. The five lung tissue patterns involved in most differential restrictive and obstructive lung disease diagnoses include: emphysema, ground glass, fibrosis, micronodule, and normal. Four established network architectures have been trained and evaluated. To the best of our knowledge, this is the first comprehensive end-to-end deep CNN pipeline for differential diagnosis of emphysema. A comparative analysis shows the performance of the proposed models on two publicly available datasets.