CNC (computer numerically controlled) machine tools are highly advanced technological systems, used to machine parts by means of metal cutting processes. Their structure and kinematics are very complex, involving accurate coordinated motions on three to five axes. Operating CNC machine tools is a complicated process, which can easily be affected by errors. Nowadays, safety systems and devices are developed in order to make this process safer and more user friendly. Modern CNC controllers are designed to deal with obvious sources of hazards, such as overloads (by means of various sensor systems) and collisions (by checking the NC code syntax and simulating it on the machine). However, despite of these safety systems, various unwanted events still occur during machining operations on CNC machine tools. These means that there are still certain hazards, not so obvious, which can severely affect the operation of CNC machine tools. This work tries to identify and hierarchize the above-mentioned hazards by using an AHP (analytic hierarchy process) approach. The results of the AHP emphasize which hazard has the biggest influence upon the CNC machine tools operation and consequently should be avoided. The results of this work could be used by the machine tools designers to develop new safety features for the existing CNC controllers. Also, the users of the machine tools could focus some of the safety measures during the machining process upon the most significant hazards pointed by the results of the research.