A method for automatic detection of a medical instrument orientation for robotic surgery is presented. The method determines the orientation of a marker device attached to the medical instrument in relation to the robotic system by comparing movement information. The method compares the information about a movement of the marker device from a tracking system with the information about a movement of the robotic arm, which movement data can be acquired by the robotic system. The orientation of the medical instrument with respect to the robotic system can be determined automatically and used for subsequent calculations such as an automatic and efficient precise alignment to a target trajectory or a correct positioning assistance for a mechatronic arm. A computer-implemented medical method of automatically determining an orientation of a medical instrument base in relation to a robotic system is provided.