We performed dedicated imputation of HLA-DRB1 and DRB3 in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort and observed a negative correlation in effect estimates between ALSPAC self-reported pertussis and the pooled PT effect estimates for HLA-DRB1 amino acids determined from the infants recruited in Uganda, Burkina Faso and South Africa (r = −0.55, Pperm < 1 × 10−5) but little evidence of correlation for HLA-DRB3 (r = 0.13, Pperm = 0.16). Here, HLA-DRB1 is linked to pertussis.