Background: The aim of this study was to estimate overall prevalence of primary headaches and prevalence of migraine (MG) and tension-type headache (TTH) among adolescents in the Republic of Moldova. Metetial and methods: In total there were 3389 adolescents whose age ranged from 10 to 19 years, recruited from urban and rural areas of the country. This school-based study was conducted during the academic year 2015-2016. The information was collected with the use of self-administered questionnaire based on the criteria of International Classification of Headache Disorders: ICHD-2 (2004) and ICHD-3 (2013). Primary headaches were classified, according to the type of headache and after the frequency of headache attacks within the month. Results: The overall prevalence of primary headaches in Moldovan adolescents is 38.75% (girls – 49.7%, boys – 27.8%), and it is higher in urban area (48.23%) than in rural (30.05%). The prevalence of MG is 19.7%. The prevalence of MG is higher in girls (27.5%) than in boys (12.1%). The prevalence of migraine is higher in urban adolescents (27.1%) compared to rural ones (13.0%). The prevalence of TTH is 7.9%. The prevalence of TTH is almost equal in both sexes (8.0% in girls and 7.7% in boys). The prevalence of TTH in urban adolescents is 10.2% and it is more than 1.7 times higher compared to the recorded level in rural areas – 5.8%. Conclusions: The present study is the first Moldovan survey on epidemiology of headaches in adolescents. It is very important to continue developing different aspects of epidemiology of adolescents’ headaches in the Republic of Moldova