Swimming pool attendance and exposure to chlorination by-products showed adverse health effects on children. We assessed whether early swimming pool attendance, especially baby swimming, is related to higher rates of early infections and to the development of allergic diseases. In 2003-2005, 2192 children were analysed for the 6-year follow-up of a prospective birth cohort study. Data on early swimming pool attendance, other lifestyle factors and medical history were collected by parental-administered questionnaire. Bivariate and multivariate logistic regression analyses were used to evaluate associations. Babies who did not participate in baby swimming had lower rates of infection in the 1st year of life (i) diarrhoea: OR 0.68 CI 95% 0.54-0.85; (ii) otitis media: OR 0.81 CI 95% 0.62-1.05; (iii) airway infections: OR 0.85 CI 95% 0.67-1.09. No clear association could be found between late or non-swimmers and atopic dermatitis or hay fever until the age of 6 years, while higher rates of asthma were found (OR 2.15 95% CI 1.16-3.99), however, potentially due to reverse causation. The study indicates that, in terms of infections, baby swimming might not be as harmless as commonly thought. Further evidence is needed to make conclusions if the current regulations on chlorine in Germany might not protect swimming pool attendees from an increased risk of gastrointestinal infections. In terms of developing atopic diseases there is no verifiable detrimental effect of early swimming.