Monitoring antigenic and genetic variations of circulating influenza viruses is critical for the selection of annual vaccine strains. In order to gain insight into the molecular evolution of Influenza B viruses (IBV) isolated in Uruguay in 2002 and 2005 outbreaks, antigenic and phylogenetic studies were carried out for the Hemagglutinin (HA) gene. Antigenic relations among Uruguayan and reference strains isolated elsewhere were performed by means of hemagglutination inhibition assays (HAI). Genetic relations of HA genes from Uruguayan as well as 41 IBV strains isolated elsewhere were established by means of the construction of phylogenetic trees. HAI assays showed a distant antigenic relationship among the 2002 Uruguayan isolates and the 2002 vaccine strain B/Sichuan/379/99. Phylogenetic analysis also revealed a distant genetic relationship among Uruguayan and 2002 vaccine strains. All 2005 IBV Uruguayan strains were both antigenically and genetically related to B/Victoria lineage-viruses. The results of these studies revealed that 2002 IBV Uruguayan strains have a distant antigenic and genetic relation with the 2002 IBV vaccine strain used in Uruguay. The high rate of susceptible individuals in the youngest cohort (<25 years) might be related to the fact that the B/Victoria lineage-viruses were not previously circulating in Uruguay.