The Human Machine Interface (HMI) of intraluminal robots has a crucial impact on the clinician's performance. It increases or decreases the difficulty of the tasks, and is connected to the users' physical and mental stress. Objective: This paper presents a framework to compare and evaluate different HMI for robotic colonoscopy, with the objective of identifying the optimal HMI that minimises the clinician's effort and maximises the clinical outcomes. Methods: The framework comprises a (1) a virtual simulator (clinically validated), (2) wearable sensors measuring the cognitive load, (3) a data collection unit of metrics correlated to the clinical performances, and (4) questionnaires exploring the users' impressions and perceived stress. The framework was tested with 42 clinicians investigating the optimal device for teleoperated control of robotic colonoscopes. Two control devices were selected and compared: a haptic serial-kinematic device and a standard videogame joypad. Results: The haptic device was preferred by the endoscopists, but the joypad enabled better clinical performance and reduced cognitive and physical load. Conclusion: The framework can be used to evaluate different aspects of HMI, both hardware and software, and determine the optimal HMI that can reduce the burden on clinicians while improving the clinical outcome. Significance: The findings of this study, and of future studies performed with this framework, can inform the design and development of HMI for intraluminal robots, leading to improved clinical performance, reduced physical and mental stress for clinicians, and ultimately better patient outcomes.