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The objective of the study was to investigate the long-term effects of maternal hepatitis B virus (HBV) or hepatitis C virus (HCV) carrier status on the long-term infectious morbidity of their offspring. A population-based cohort study was conducted, including all singleton deliveries between the years 1991 and 2014 at a tertiary medical centre. The mothers were subdivided into three groups: HBV carriers, HCV carriers and non-carriers. Data on demographics, maternal, perinatal and long-term hospitalization for infectious morbidity were compared between the groups. During the study period, 242 905 (99.7%) non-carrier mothers, 591 (0.2%) HBV carriers and 186 (0.1%) HCV carriers were observed. Hospitalizations related to infectious morbidity was significantly higher in the offspring of HBV carriers compared with HCV and non-carriers (15.6% vs 11.3% vs 11.0%; P = .002, respectively; Kaplan-Meier, log-rank P < .001). Specifically, a significantly higher rate of hospitalizations gastrointestinal infectious morbidity was noted among the offspring of HBV carrier mothers (3.6% in the HBV carrier group, 1.6% in the HCV carrier group and 1.6% in the non-carrier group [P = .001]). There was a respiratory infectious morbidity of 8.1% among the offspring of HBV carriers, 8.6% among HCV carriers and 5.5% in non-carriers (P = .005). Using a Cox multivariable model, controlling for confounding variables, maternal HBV carrier status was associated with a significantly increased long-term infectious morbidity of the offspring, with an adjusted HR of 1.7 (95% CI, 1.388-2.077, P < .001). Maternal HBV carrier status is an independent risk factor for long-term infectious morbidity of the offspring, particularly for gastrointestinal and respiratory infections., (© 2020 John Wiley & Sons Ltd.)