The technology relates to autonomous vehicles having articulating sections such as the trailer of a tractor-trailer. Aspects include approaches for tracking the pose of the trailer, including its orientation relative to the tractor unit. Sensor data is analyzed from one or more onboard sensors to identify and track the pose. The pose information is usable by on-board perception and/or planning systems when driving the vehicle in an autonomous mode. By way of example, on-board sensors such as Lidar sensors are used to detect the real-time pose of the trailer based on Lidar point cloud data. The orientation of the trailer is estimated based on the point cloud data, and the pose is determined according to the orientation and other information about the trailer. Aspects also include determining which side of the trailer the sensor data is coming from. A camera may also detect trailer marking information to supplement the analysis.