Background Infectious disease (ID) hospitalisation rates are increasing in New Zealand (NZ), especially in preschool children, and Māori and Pacific people. We aimed to identify risk factors for ID hospitalisation in infancy within a birth cohort of NZ children, and to identify differences in risk factors between ethnic groups. Methods We investigated an established cohort of 6846 NZ children, born in 2009-10, with linkage to a national dataset of hospitalisations. We used multivariable logistic regression to obtain odds ratios (OR) for factors associated with ID hospitalisation in the first year of life, firstly for all children, and then separately for Māori or Pacific children. Results In the whole cohort, factors associated with ID hospitalisation were Māori (OR=1.49, 95%CI 1.17-1.89) or Pacific (2.51, 2.00-3.15) vs. European maternal ethnicity, male gender (1.32, 1.13-1.55), low birthweight (1.94, 1.39-2.66), exclusive breastfeeding for <4 months (1.22, 1.04-1.43), maternal experience of healthcare racism (1.60, 1.19-2.12), household deprivation (most vs. least deprived quintile of households [1.50, 1.12-2.02]), day-care attendance (1.43, 1.12-1.81), and maternal smoking (1.55, 1.26-1.91). Factors associated with ID hospitalisation for Māori infants were: high household deprivation (2.16, 1.06-5.02) and maternal smoking (1.48, 1.02-2.14); and for Pacific infants: delayed immunization (1.72, 1.23-2.38), maternal experience of healthcare racism (2.20, 1.29-3.70), and maternal smoking (1.59, 1.10-2.29). Conclusions: Māori and Pacific children in NZ experience a high burden of ID hospitalisation. Some risk factors, for example maternal smoking, are shared while others are ethnic-specific. Interventions aimed at preventing ID hospitalisations should address both shared and ethnic-specific factors.</p