Among the various applications of virtual reality (VR) systems, during the last fifteen years there has been a noticeable evolution of applications related to the assessment and therapy of physical and psychological disorders. In these VR systems, supervisor sometimes performs manual adaptation of a virtual environment according to the subject’s characteristics, to improve quality and efficiency of the procedure to which the system is being applied. Certain objective practical limitations of manual adaptation stress the need for introducing the complementary automated adaptation. The master’s thesis gives overview of the fields of whiplash injury diagnosis and therapy of posttraumatic stress disorder (PTSD), emphasizing existing research related to application of VR technology in these fields. Assessment of neck functional difficulties and the exposure therapy of PTSD are attended to in more detail. In the technical review part of the thesis, existing architectures of VR systems and adaptive control systems are described, which form foundation for automated-manual adaptive control of scenarios in supervisor-subject VR systems. The central part of the thesis proposes generic concept of automated-manual adaptive control of scenarios in supervisor-subject VR systems. A description of functional and concurrency structure of the generic concept is given, applying existing architectures and structuring methods of VR systems and adaptive control systems. Control-stimulation logic of the generic concept is mapped to two medical application domains that have been introduced in the medical review part of the thesis: functional assessment of whiplash injuries, and exposure therapy of PTSD. Proposed structure of the control-stimulation logic of the generic concept is sufficiently expressive to encompass existing supervisor’s manual adaptation of virtual environment in the mentioned application domains. For each application domain, applicable mechanisms of automated adaptation are described, as well as the parts of the structure of the generic concept that support embedding of these mechanisms.