Early detection of lung cancer can help in a sharp decrease in the lung cancer mortality rate, which accounts for more than 17% percent of the total cancer related deaths. A large number of cases are encountered by radiologists on a daily basis for initial diagnosis. Computer-aided diagnosis (CAD) systems can assist radiologists by offering a "second opinion" and making the whole process faster. We propose a CAD system which uses deep features extracted from an auto encoder to classify lung nodules as either malignant or benign. We use 4303 instances containing 4323 nodules from the National Cancer Institute (NCI) Lung Image Database Consortium (LIDC) dataset to obtain an overall accuracy of 75.01% with a sensitivity of 83.35% and false positive of 0.39/patient over a 10 fold cross validation.