Arguably, the most challenging emergencies encountered by emergency medical service crews involve children. Because only scant data exist about the epidemiology of pediatric emergencies in helicopter emergency medical service (HEMS) on a population level, we sought to determine the epidemiological characteristics stratified by responding area in a large nationwide sample. This was a retrospective cohort study including all pediatric patients (0-14 years of age) who were treated by HEMS in Austria from January 2006 to June 2007 (18 months). Pediatric emergencies accounted for 2207 (8.2%) of a total of 26.850 helicopter rescue missions. Of those, 69.9% (n = 1543) were not involved in life-threatening emergencies. The rate of critical pediatric emergencies was higher in urban than in rural or alpine environment (45.2%, 38.2% and 20.3%, respectively). The most common chief complaint was trauma; the frequency of injuries ranged from 54.2% (582/1074) in rural area and 60.3% (44/73) in urban area to 91.4% (969/1060) in alpine environment. Fracture and head trauma (34.9%; 557/1595 and 26.3%; 419/1595, respectively) were the most common injuries. Advanced life support measures like tracheal intubation, cardiopulmonary resuscitation and intraosseous access were rarely performed (3.7%; n = 82, 1.9%; n = 42 and 0.9%; n = 19, respectively). Pediatric emergencies in Austrian HEMS show different epidemiological characteristics in alpine, urban and rural operational environments. Because of challenges and infrequency of prehospital pediatric emergencies, HEMS crews need to maintain their skills in pediatric advanced life support and trauma care.