Abstract Background Ireland has one of the lowest BF rates in the world. This study investigates the association between breastfeeding and infant health in Ireland. Methods A cross-sectional, secondary analysis of data collected from Growing Up in Ireland (GUI): the National Longitudinal Study of Children was conducted. The average morbidity for 2212. infants exclusively breastfed for at least 90 days (EBF90days) was compared to data for 3987 infants in the non-breastfed (Non-BF) group. Data were weighted using entropy balancing to ensure the comparability of groups. Sensitivity analyses considered alternative definitions of the breastfeeding group. Results Infants who were EBF90days were significantly less likely to be admitted to hospital (CI: − 0.06 to − 0.03), spent less nights in hospital (CI: − 0.37 to − 0.11), and were less likely to develop respiratory diseases including asthma (CI: − 0.03 to − 0.01), chest infections (CI: − 0.12 to − 0.08), snuffles/common colds (CI: − 0.07 to − 0.02), ear infections (CI: − 0.08 to − 0.04), eczema (CI: − 0.08 to − 0.04), skin problems (CI: − 0.04 to − 0.00), wheezing or asthma (CI: − 0.06 to − 0.03), vomiting (CI: − 0.03 to − 0.00), and colic (CI: − 0.04 to − 0.01). Further outcomes such as current health of the infant at time of interview (CI: − 0.04 to − 0.00), feeding problems (CI: − 0.04 to − 0.02) and sleeping problems (CI: − 0.02 to − 0.00) indicated a protective effect of EBF90days versus Non-BF. However, these infants were also more likely to fail to gain weight (CI: 0.01 to 0.02) and were at a slightly higher risk of developing nappy rash (CI: 0.00 to 0.02). Conclusion Exclusive breastfeeding for 90+ days is associated with protection against childhood morbidity. Given the protective effect of breastfeeding on adverse health effects in infants, policy makers should prioritise policies that support, promote and protect exclusive breastfeeding.