Condition monitoring and fault diagnosis are important for maintaining the system performance and guaranteeing the operational safety. The traditional data-driven approaches mostly incorporate well-defined features and methodologies such as supervised artificial intelligence algorithms. Prior knowledge of possible features and a large quantity of labelled condition data are needed. Besides, many traditional approaches require rebuilding or a retraining of the original model to diagnosis new conditions. The present study proposes an intelligent fault diagnosis approach that uses a deep neural network (DNN) based on stacked denoising autoencoder. Representative features are learned by applying the denoising autoencoder to the unlabelled data in an unsupervised manner. A DNN is then constructed and fine-tuned with just a few items of labelled data. The trained DNN achieves high performance in fault classification. Furthermore, new conditions can be correctly classified by simply fine-tuning the trained DNN model using a small amount of labelled data under the new conditions. The effectiveness of the proposed approach is evaluated using a case study of fault diagnosis of a bearing unit. The results indicate that the proposed method can extract representative features from massive unlabelled data on the system condition and achieve high performance in fault diagnosis.