We are developing a U-Net based deep learning (U-DL) model for bladder segmentation in CT urography (CTU) as a part of a computer-assisted bladder cancer detection and treatment response assessment pipeline. We previously developed a bladder segmentation method that used a deep-learning convolution neural network and level sets (DCNNLS) within a user-input bounding box. The new method does not require a user-input box nor the level sets for postprocessing. To identify the best model for this task, we compared a number of U-DL models: 1) 2D CTU slices or 3D volume as input, 2) different image resolutions, and 3) preprocessing with and without automated cropping on each slice. We evaluated the segmentation performance of the different U-DL models using 3D hand-segmented contours as reference standard. The segmentation accuracy was quantified by the average volume intersection ratio (AVI), average percent volume error (AVE), average absolute volume error (AAVE), average minimum distance (AMD), and the Jaccard index (JI) for a data set of 81 training/validation and 92 independent test cases. For the test set, the best 2D UDL model achieved AVI, AVE, AAVE, AMD, and JI values of 93.4±9.5%, -4.2±14.2%, 9.2±11.5%, 2.7±2.5 mm, 85.0±11.3%, respectively, while the best 3D U-DL achieved 90.6±11.9%, -2.3±21.7%, 11.5±18.5%, 3.1±3.2 mm, and 82.6±14.2%, respectively. For comparison, the corresponding values obtained with our previous DCNN-LS method were 81.9±12.1%, 10.2±16.2%, 14.0±13.0%, 3.6±2.0 mm, and 76.2±11.8%, respectively, for the same test set. The UDL model provided highly accurate bladder segmentation and was more automated than the previous approach.