This study was conducted within the Growing Up in New Zealand (GUiNZ) longitudinal birth cohort, which enrolled 6,822 pregnant women in the Auckland, Counties-Manukau and Waikato District Health Board areas due to deliver in 2009 or 2010. The GUiNZ cohort includes representative proportions of Māori, Pacific, and socioeconomically deprived families. This analysis of GUiNZ data reports rates of hospitalisation for an infectious disease (ID) within the first 5 years of life, an outcome that is known to be linked to greater socioeconomic deprivation. Using only cross-sectional data at 4.5 years of child age, this analysis included 5,602 children and compared different methods of ethnicity and socioeconomic deprivation, to determine the most accurate measures. Primary caregivers assigned the children to either a self-prioritised ethnicity (i.e. the main ethnic group with which their child identified), a total response ethnicity (i.e. the ethnic group or groups their child belonged to), or single-combined ethnic groups (i.e. assigning the child to a single or combination ethnic group matching their combination of ethnicities). Socioeconomic status was measured using household income, census-derived and survey-derived deprivation indices. The easiest category of child ethnicity to analyse was the self-prioritisation group. Total response was complicated by mixed ethnicity allowing overlap between groups. The researchers had to aggregate small groups for the single-combined ethnicity cohort to maintain statistical power, but this measure offered greater detail. Whichever method was used to ascribe ethnicity, Māori and Pacific children were at greater risk of ID hospitalisation, as were children in the most socioeconomically deprived households. The magnitude of these effects differed according to whichever methodology was used. Household income was affected by non-random missing data. The census-derived deprivation index offered a high level of completeness with some risk of multicollinearity and concerns regarding the ecological fallacy (i.e. making assumptions about individuals within a given decile). The survey-derived index contained an additional 8 questions but proved acceptable to participants and provided individualised data, so largely avoided the ecological fallacy concerns affecting the censusderived deprivation index.