Deformable image registration is usually performed manually by clinicians,which is time-consuming and costly, or using optimization-based algorithms, which are not always optimal for registering images of different modalities. In this work, a deep learning-based method for MR-CT deformable image registration is presented. In the first place, a neural network is optimized to register CT pelvic image pairs. Later, the model is trained on MR-CT image pairs to register CT images to match its MR counterpart. To solve the unavailability of ground truth data problem, two approaches were used. For the CT-CT case, perfectly aligned image pairs were the starting point of our model, and random deformations were generated to create a ground truth deformation field. For the multi-modal case, synthetic CT images were generated from T2-weighted MR using a CycleGAN model, plus synthetic deformations were applied to the MR images to generate ground truth deformation fields. The synthetic deformations were created by combining a coarse and fine deformation grid, obtaining a field with deformations of different scales. Several models were trained on images of different resolutions. Their performance was benchmarked with an analytic algorithm used in an actual registration workflow. The CT-CT models were tested using image pairs created by applying synthetic deformation fields. The MR-CT models were tested using two types of test images. The first one contained synthetic CT images and MR ones deformed by synthetically generated deformation fields. The second test set contained real MR-CT image pairs. The test performance was measured using the Dice coefficient. The CT-CT models obtained Dice scores higherthan 0.82 even for the models trained on lower resolution images. Despite the fact that all MR-CT models experienced a drop in their performance, the biggest decrease came from the analytic method used as a reference, both for synthetic and real test data. This means that the deep learning models outperformed the state-of-the-art analytic benchmark method. Even though the obtained Dice scores would need further improvement to be used in a clinical setting, the results show great potential for using deep learning-based methods for multi- and mono-modal deformable image registration.