Systems and methods for collision detection and avoidance are provided. In one aspect, a robotic medical system including a first set of links, a second set of links, a console configured to receive input commanding motion of the first set of links and the second set of links, a processor, and at least one computer-readable memory in communication with the processor. The processor is configured to access the model of the first set of links and the second set of links, control movement of the first set of links and the second set of links based on the input received by the console, determine a distance between the first set of links and the second set of links based on the model, and prevent a collision between the first set of links and the second set of links based on the determined distance.