Immunoglobulin (Ig) E may provide immunity against Borrelia burgdorferi infection (Lyme disease) in children which lasts throughout adulthood. We investigated the presence and persistence of IgE anti‐B. burgdorferi antibodies (Abs) in paediatric patients infected with Lyme disease over time. Serum immunoglobulin levels, presence of IgG and IgE anti‐B. burgdorferi components, and distributions of blood T, B and natural killer lymphocyte subsets were studied in B. burgdorferi‐infected and ‐uninfected children (nephelometry, UniCAP Total IgE Fluoroenzymeimmunoassay, Western blot, flow cytometry). Total serum IgM, IgG, IgE and IgA levels, and distributions of blood lymphocytes (CD4+, CD8+, CD19+) of both groups, excluding CD8+CD60+ T cells, were within normal ranges. However, infected, but not uninfected children made IgG anti‐B. burgdorferi proteins p18, p31, p34, p41, p45, but not IgG anti‐p60, and IgE anti‐B. burgdorferi proteins p31, p34, p41, p45, p60, but not IgE anti‐p18. These proteins were also detected in an infected child 1 year post‐infection. Interestingly, CD8+CD60+ T‐cell numbers were significantly increased (fourfold) in infected, compared with uninfected, patients (P = 0.001). These results demonstrate that specific IgE anti‐B. burgdorferi Abs are generated and persist in children with Lyme disease and that CD8+CD60+ T cells may play an important role in these responses.