Quantitative assessment of immunogen‐specific T cell responses may provide a meaningful surrogate marker of functional immunity in patients following haemopoietic stem cell transplantation (HSCT). We developed a flow‐cytometric assay to quantify antigen‐specific T cell immunity to influenza‐A and studied the T cell response to influenza vaccination in five children, 3–21 months post‐HSCT. All patients showed an increase in influenza‐A‐specific CD4⁺ immunity following vaccination while none had a detectable IgG response to the vaccine. This assay proved sufficiently sensitive to evaluate changes in T cell memory in immunocompromised individuals and could be used to better characterize post‐HSCT immune reconstitution.