What is known: • The use of antibiotics early in life has been associated with an increased risk of developing atopic dermatitis or asthma. • Confounding by indication or reverse causation may underlie the observed associations.

What is new: • Our results demonstrate that neonatal antibiotic therapy for confirmed or clinically diagnosed infection was associated with increased risk of atopic dermatitis and antibiotic treatment before six months of age was associated with atopic dermatitis, asthma and inhaled corticosteroid use in analyses adjusted for confounding factors.