Aspects of the disclosure relate to repositioning a rooftop sensor of an autonomous vehicle when needed to reduce the overall height of the autonomous vehicle. For instance, while an autonomous vehicle is being controlled in an autonomous driving mode, a low clearance zone may be identified. An activation location may be determined based on the low clearance zone and a current speed of the autonomous vehicle. Once the activation location is reached by the autonomous vehicle, a motor may be caused to reposition the rooftop sensor. In addition, in some instances, after the autonomous vehicle has passed the low clearance zone, the motor may be caused to reposition the rooftop sensor again.