Estimated associations between infections with different helminth species can be used to predict the proportion of a population infected with multiple species infections. This is an important measure of disease burden, as those with multiple infections are often at an increased risk of morbidity. In this paper, we investigate variation amongst the estimated associations between Ascaris lumbricoides, Trichuris trichiura and hookworm, over a number of different spatial levels among schoolchildren in Cameroon. Associations between species were largely homogeneous within districts, provinces and ecological zones, although variation between these regions was identified, implying that a single measure of association may not be appropriate in different epidemiological settings. Further data collected amongst school children in Kenya and Uganda were analysed, to assess the dependence of the associations on the intensity of infection. It was found that the strength of the association between A. lumbricoides and T. trichiura increased with intensity, such that those with more intense infections with one species are increasingly likely to harbour concurrent intense infections with the other species. The implications of these results are discussed in relation to the estimation of the disease burden due to multiple helminth species.