The importance of host heterogeneity in generating aggregation was investigated using Heligmosomoides polygyrus (Nematoda) in laboratory mice. Parameters of infection were compared between inbred and outbred mice, between primary and challenge infection protocols, and between gavage and natural exposure protocols, to investigate the relative effects of innate resistance, acquired resistance and behaviour, respectively. Heterogeneity in acquired resistance was identified as the most consistent factor leading to variability and aggregation of H. polygyrus numbers in mice. This hypothesis was supported in two experiments where groups of mice did not develop resistance to challenge infection (use of certain inbred strains of mice and immunosuppression with corticosteroids in the drinking water) and where variability in worm numbers after the challenge infection was comparable with that after the primary infection. Heterogeneity in host behaviour, particularly in behaviours enhancing skin contact with larvae, also was associated with increased heterogeneity in worm burden, though not as consistently as heterogeneity in acquired resistance. Surprisingly, worm burdens were not more variable in outbred compared with inbred mice. Our data suggest that the relative contributions of innate resistance, acquired resistance and behaviour in generating variable worm burdens are likely to vary spatially and temporally.