The KUNO-Kids birth cohort study was established to investigate various aspects of child health, using novel omics technologies in a systems medicine approach. After 3 years of recruitment, 2,515 infants and their families have joined the study, which is based in Eastern Bavaria in Regensburg, Germany. KUNO-Kids aims to investigate a wide range of exposures and outcomes. Data are collected not only from the index child (or children in the case of multiples), but also from his/her family. The inclusion in the study starts immediately after birth of the index child. The baseline assessment takes place during the short hospital stay of the mother and child directly after birth. Regular follow-up assessments are conducted when the index child is 4 weeks old, 6 months old, and at each birthday. At baseline, the mothers’ mean age was 33.9 years, and 56% gave birth for the first time.