Newly created software is presented in magister degree thesis. The software was created for the innovative non–invasive cerebral blood flow autoregulation monitor which has no analogy in the global high tech market. It will be possible at first time to get diagnostic information about the cerebral blood flow autoregulation status of patient with severe brain injuries using such non–invasive monitoring technology in clinical practice. That will help with the individual treatment decision making. Clinical studies were conducted in neurosurgical intensive care units using created software. It has been shown that non–invasive and invasive cerebrovascular blood flow autoregulation monitoring technologies provide the same diagnostic information about the patient status. That conclusion is statistically significant and evidence based. Some R & D projects were performed using non–invasive cerebrovascular blood flow autoregulation monitor with implemented new software. The results of such projects were used in order to formulate the metrological – technological requirements for the final design and development of the innovative non–invasive blood flow autoregulation monitor. Such device is under creation in Telematics Scientific Laboratory which works together with Vittamed Technologijos Ltd and conducts 6.015 million Lt project (BPD04-ERPF-3.1.7-03-05/0020).