Infectious bursal disease virus (IBDV) is an immunosuppressive virus which primarily infects IgM B-cells in the bursa of Fabricius. Flow cytometric analysis was used to phenotype B-cell populations in the bursa and spleen following IBDV infection. In the bursa, two IgM B-cell subpopulations, designated as A and B, were identified based on cell size and granularity. While both subpopulations differentially expressed IgM and Bu-1b surface markers, both groups displayed major histocompatibility complex class II surface antigens at equal levels. Following IBDV challenge of nonvaccinated birds, the B subpopulation was significantly reduced between 7 and 21 days postchallenge compared to either nonchallenged birds or vaccinated–challenged birds. However, the reduction of subpopulation B in the bursa, following IBDV exposure, did not reduce the levels of total serum IgA, IgG, and IgM, nor did it affect IgG and IgA B-cells in the spleen. Phenotypic analysis of the subpopulations identified differential expression of Lewis^x, IgM, Bu-1b, and MUI78 surface antigens between the subpopulations. Overall, these are the first studies to identify two distinct IgM B-cell subpopulations in the chicken bursa, and the first to describe the decrease in the IgM B-cell population relative to IgA and IgG B-cells following IBDV infection.