The role of aluminium for IgG and IgE responses to pertussis toxin (PT), as well as for side effects, was investigated in 49 children with known atopy status. Primary immunization had been given with an adsorbed monocomponent or an adsorbed two-component acellular pertussis vaccine. The children were then randomized to receive a booster immunization with either aluminium-adsorbed or non-adsorbed, whole cell, pertussis vaccine. Both vaccines induced good IgG responses with the adsorbed vaccine giving higher post-booster levels (p < 0.05). The adsorbed vaccine was, however, associated with more local side effects (p < 0.05) and tended to induce higher PT-IgE responses than the non-adsorbed vaccine. Furthermore, individuals who had received the two-component vaccine as primary immunization had higher PT-IgE responses after the booster, compared with individuals initially receiving the monocomponent vaccine (p = 0.041). No correlation between PT-IgE and PT-IgG levels was seen in any of the groups. Total serum IgE levels correlated to PT IgE levels, particularly in children with atopy (r = 0.950, p < 0.001). The addition of aluminium to the pertussis vaccine, was, thus, associated with a stronger IgG antibody response, but tended also to induce a stronger IgE antibody response. The correlation between total IgE and PT-IgE, which was most prominent in children with atopy, indicates that the role of immunization for the development of allergy merits further studies.