Human enterovirus 109 (EV109) is a recently identified recombinant enterovirus in family Picornaviridae from acute paediatric respiratory illness in Nicaragua. EV109 have not been reported elsewhere. Our aims were the molecular detection and genetic analysis of EV109 from acute childhood respiratory infections in Hungary. Nasopharyngeal aspirates were collected from children under age of 10 years with acute respiratory infections treated in Department of Pulmonology, Kaposi Mór Teaching Hospital, Mosdós, Hungary. Samples were taken from 15 October to 15 May in two respiratory seasons 2005/2006 and 2006/2007. Samples were tested using EV109 specific VP1 primers by RT-PCR method. One (1.1%) of the 92 nasopharyngeal aspirates was positive for EV109 collected from a 2.5-year-old child in January, 2007. The main symptoms were dropping nose, fever (38.1°C), hard cough and wheezing associated with bronchitis and pneumonia. Based upon the VP1 gene region EV109 (L87/HUN/2007, JN900470) has 93% nucleotide identity and identical recombinant pattern to the prototype EV109. This is the first detection of the novel recombinant enterovirus, EV109, in Hungary (in Europe). This study supports the possibility that EV109 is able to cause acute respiratory infections, in addition, it might be plays a part in lower respiratory disease with hospitalization in children.