Low serum levels of mannose-binding lectin (MBL) have been associated with recurrent infections in early childhood. Otitis media (OM) is frequent in Greenlandic children and the first episode of acute OM (AOM) occurs early as is the case also with Epstein-Barr virus (EBV) infection. We have therefore investigated the association between MBL genotypes, episodes of AOM, and early EBV infection in 82 community-based, unselected children in Greenland. Nasopharyngeal aspirations for EBV and MBL genotype examination, nasopharyngeal bacterial cultures, and history of AOM episodes were obtained. MBL genotypes were established in 73 specimens: 68% of these were homozygous for normal wildtype (AA), and 32% were homozygous or heterozygous for variant alleles that are associated with absence or low MBL serum level. The allele frequencies were: A = 0.88, B = 0.08 (codon 54) and D = 0.04 (codon 52). EBV was found in 41 specimens, more often with increasing age, and significantly related to ethnicity. Presence of variant MBL alleles or EBV infection was not associated with AOM, recurrent AOM (rAOM) or age at first AOM episode and EBV positive children with homozygosity for the normal MBL genotype did not have significantly more episodes of AOM, rAOM or earlier age at the first AOM episode. MBL genotypes and EBV infection alone or in interplay are not associated with the high prevalence of OM in Greenlandic children. The study suggests that low MBL level does not by itself predispose to AOM in community-based, unselected children.