Memory B cell defects underlying the increased susceptibility to infection by encapsulated bacteria have been examined in allogeneic haematopoetic stem cell transplant (HSCT) recipients. Circulating IgM memory B cells (CD19⁺, CD27⁺, IgM⁺) and switched memory B cells (CD19⁺, CD27⁺, IgM^-) were enumerated in allogeneic HSCT recipients (n=38) and healthy controls (n=35). T lymphocyte subpopulations and serum levels of immunoglobulins, including IgG subclasses, and antibodies to pneumococcal polysaccharides were also assayed. Allogeneic HSCT recipients were deficient in both switched memory and IgM memory B cells as compared to healthy controls (both P < 0.0001), irrespective of time post HSCT. Switched memory B cell deficiency correlated with CD4⁺ T cell deficiency and both correlated with serum levels of IgG1 (P < 0.0001), possibly reflecting impaired B cell isotype switching in germinal centres. ‘Steady state’ serum levels of antibodies to pneumococcal polysaccharides did not correlate with circulating memory B cells. Graft versus Host Disease (GvHD) was associated with lower IgM memory B cell counts and lower serum levels of IgG2, IgG4, IgA and pneumococcal antibodies. The increased susceptibility of allogeneic HSCT patients to infection by encapsulated bacteria may reflect a combination of memory B cell defects, which are most common in patients with a history of GvHD.