Aim of the study: Dengue infection occurs almost all over subtropical and tropical countries. Dengue pathogenesis explaining its clinical manifestations is still unclear. Indonesia is a country with several hyperendemic regions. The study was aimed to investigate the incidence rate, sero-epidemiology, and the relationship between the serotype and the clinical severity of dengue viral infection in paediatric patients from Gondokusuman, Yogyakarta. Material and methods: It was an epidemiological research with prospective observational design reviewing febrile paediatric patients involved in “A Prospective Sero-epidemiology Study on Dengue Children Infection in Yogyakarta, Indonesia, 1995–1999 cohort study.” Febrile paediatric patients were diagnosed for dengue fever, dengue haemorrhagic fever, or dengue shock syndrome based on World Health Organization 1997 criteria. Serological diagnosis was performed using PRNT and serotype identification was performed by viral culture isolation and RT-PCR. Results: Laboratory data (PRNT, ELISA, RT-PCR and Isolation) showed that there were 220 children (130 males and 90 females) from 509 febrile patients among 2,149 paediatric subjects who were infected with dengue virus. Based on serotype identification, the following dengue virus serotype distributions were identified: DEN-1 26.81%, DEN-2 23.18%, DEN-3 22.72%, DEN-4 8.63%, and unidentified 18.63%. Clinical severities observed were as follows: dengue fever 78.6%, dengue haemorrhagic fever 18.2%, and dengue shock syndrome 3.2%. In the case of primary infection, only DEN-3 could cause severe clinical manifestations. Conclusions: Gondokusuman region in Yogyakarta could be classified as a hyperendemic region between 1995 and 1999, with the highest risk of severe clinical manifestations shown for DEN-3 during both, primary and secondary infection.