Introduction As well as other countries, helicopter emergency medical service (HEMS) with physicians is one of the most important medical resources for emergency medical services in Japan. In previous studies, however, the effectiveness of HEMS has remained controversial. The aims of this study are to analyze the medical and economical effectiveness of HEMS as an example using database of HEMS of Toyama Prefecture in Japan. And factors affected to patient's outcome, survival after transported to hospital, were also analyzed. Methods We used database of HEMS of Toyama that registered all HEMS transported patient's records. The period in the analysis is from September 1, 2015 to March 31, 2017. Among them, we use patients with serious conditions and following data were excluded in advance; 1) patients diagnosed with cardiopulmonary arrest when the helicopter arrived, 2) patients requested from Tateyama Fire Department, because requests dispatch HEMS from Tateyama mountain range area are considered special cases, and thus not applicable for analysis with other requests, 3) patients transported from hospital to other hospital. To clarify the medical effectiveness, we compared transport time and survival rate of HEMS with grand medical emergency services (GEMS). Transport time was defined as time from receiving a call for emergency to start of physician treatment. Transport time of HEMS was measured from receiving a call for emergency to physician's contact on scene. Transport time of GEMS was estimated time of from receiving a call for emergency to arrival at hospital by emergency medical technicians, referring a web map server, if patients had been transferred by ambulance. Survival was defined according with patient's condition during three month from the onset. We compared survival by HEMS and expected survival by GEMS assuming the same period. The cost effectiveness was calculated by exogenous and endogenous diseases respectively by using following formulation; number of life years by 67 year-old from the onset was counted each patient, then total life years of each disease category were summed up. Next, total quality adjustment life years (QALYs) were calculated using the utility value, which mean patients' quality of life in extended life, e.g., recover is 1, disability is 0.5, and dead is 0. Total cost of each disease category was calculated by multiplying both overall QALYs and cost per year. The cost effectiveness of each disease category was finally summed up to obtain the overall cost -effectiveness. Lastly, factors affected on patient's outcome were analyzed. Death was defined as main outcome. Simple binary logistic regression was used to run a multivariate analysis on confounding variables of the differences of transport time between helicopter and ambulance, disease category, gender and age. Results Ultimately, 263 subjects were conducted in the study, including those with exogenous disease (e.g., trauma, n=75 and other, n=9) and endogenous disease (e.g., stroke, n=62 and other, n=117). HEMS had shortened transport time approximately 17 mins. HEMS improved outcome 25 % of whole patients. The overall cost-effectiveness of HEMS is estimated 15 million dollars, which is 10 million dollars per a year. According to the logistic regression analysis, reducing transport time by transferring with helicopter showed low mortality (odds 0.89, 95% interval confidence 0.77-0.98). Conclusion Based on this study, HEMS of Toyama showed effective medical and economical effects. HEMS staff recognize that early treatments and rapid transports improve patient's outcome. In case of Toyama, HEMS staff effort to contact patients rapidly, and start critical treatments as soon as possible after arrival on scene, and to minimum the staying time. Moreover, all hospitals in Toyama receive patients for treating optimal care immediately along with patient's conditions. Those efforts could lead to the result.