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Viral epidemiology is determined by the movement of infected people within and between geographical areas. The genetic characterization of wild-type isolates combined with standard epidemiological methods may enable the identification of the source and transmission pathways and permit differentiation between indigenous and imported viruses. We investigated the genetic characteristics of the wild-type measles virus isolated in Croatia during a 2003-2004 outbreak. The results of this study indicate the presence of the D4 measles virus genotype in Europe. The isolated virus is closely related to virus isolates from the India-like subgroup of the D4 measles virus genotype. The virus responsible for this outbreak differs in the hemagglutinin gene sequence from other virus strains belonging to the D4 genotype. The hemagglutinin gene sequence also differs when compared to viruses from other genotypes that are known to circulate in Europe and from vaccine strains.