In the last two decades, we have seen an amazing development of image processing techniques targeted for medical applications. We propose multi-GPU-based parallel real-time algorithms for segmentation and shape-based object detection, aiming at accelerating two medical image processing methods: automated blood detection in wireless capsule endoscopy (WCE) images and automated bright lesion detection in retinal fundus images. In the former method we identified segmentation and object detection as being responsible for consuming most of the global processing time. While in the latter, as segmentation was not used, shape-based object detection was the compute-intensive task identified. Experimental results show that the accelerated method running on multi-GPU systems for blood detection in WCE images is on average 265 times faster than the original CPU version and is able to process 344 frames per second. By applying the multi-GPU framework for bright lesion detection in fundus images we are able to process 62 frames per second with a speedup average 667 times faster than the equivalent CPU version.