Impaired immunity to infectious organisms contributes to the poor outcome after haemopoietic stem cell transplantation (HSCT) (Ochs et al, 1995; Chakrabarti et al, 2002; Martelli & Reisner, 2002; Veys et al, 2003). Vaccination has been used to improve immune function but the optimal vaccination strategy has not been identified and little attention has been directed at assessing the T cell response to vaccines (Avigan et al, 2001). We describe here a sensitive technique for quantifying and characterizing antigen-specific T cells that was used to measure T cell immunity to influenza A in normal adults and children, and influenza vaccination response in paediatric HSCT patients.