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Delineation of the clinical target volume (CTV) and organs at risk (OARs) is very important for radiotherapy but is time-consuming and prone to inter-observer variation. Here, we proposed a novel deep dilated convolutional neural network (DDCNN)-based method for fast and consistent auto-segmentation of these structures.Our DDCNN method was an end-to-end architecture enabling fast training and testing. Specifically, it employed a novel multiple-scale convolutional architecture to extract multiple-scale context features in the early layers, which contain the original information on fine texture and boundaries and which are very useful for accurate auto-segmentation. In addition, it enlarged the receptive fields of dilated convolutions at the end of networks to capture complementary context features. Then, it replaced the fully connected layers with fully convolutional layers to achieve pixel-wise segmentation. We used data from 278 patients with rectal cancer for evaluation. The CTV and OARs were delineated and validated by senior radiation oncologists in the planning computed tomography (CT) images. A total of 218 patients chosen randomly were used for training, and the remaining 60 for validation. The Dice similarity coefficient (DSC) was used to measure segmentation accuracy.Performance was evaluated on segmentation of the CTV and OARs. In addition, the performance of DDCNN was compared with that of U-Net. The proposed DDCNN method outperformed the U-Net for all segmentations, and the average DSC value of DDCNN was 3.8% higher than that of U-Net. Mean DSC values of DDCNN were 87.7% for the CTV, 93.4% for the bladder, 92.1% for the left femoral head, 92.3% for the right femoral head, 65.3% for the intestine, and 61.8% for the colon. The test time was 45 s per patient for segmentation of all the CTV, bladder, left and right femoral heads, colon, and intestine. We also assessed our approaches and results with those in the literature: our system showed superior performance and faster speed.These data suggest that DDCNN can be used to segment the CTV and OARs accurately and efficiently. It was invariant to the body size, body shape, and age of the patients. DDCNN could improve the consistency of contouring and streamline radiotherapy workflows.