We developed a novel ensemble three-dimensional residual network (E3D-ResNet) for the reduction of false positives (FPs) in computer-aided detection (CADe) of polyps on CT colonography (CTC). To capture the volumetric multiscale information of CTC images, each polyp candidate was represented with three different sizes of volumes of interest (VOIs), which were enlarged to a common size and were individually subjected to three 3D-ResNets. These 3D-ResNets were trained to calculate three polyp-likelihood probabilities, p1, p2 and p3, corresponding to each input VOI. The final polyp likelihood, p, was obtained as the maximum of p1, p2 and p3. We compared the classification performance of the E3D-ResNet with that of a non-ensemble 3D-ResNet, ensemble 2D-ResNet, and ensemble of 2D- and 3D-convolutional neural network (CNN) models. All models were trained and evaluated with 21,021 VOIs of polyps and 19,557 VOIs of FPs that were sampled with data augmentation from the CADe detections on the CTC data of 20 patients. We evaluated the classification performance of the models with receiver operating characteristics (ROC) analysis using cross-validation, where the area under the ROC curve (AUC) was used as the figure of merit. Preliminary results showed that AUC value (0.98) of the E3D-ResNet was significantly higher than that of the reference models (P < 0.001), indicating that the E3D-ResNet has the potential of substantially reducing the FPs in CADe of polyps on CTC.