Moraxella catarrhalis is an established bacterial pathogen, previously thought to be an innocent commensal of the respiratory tract of children and adults. The objective of this study was to identify significant risk factors associated with M. catarrhalis colonization in the first year of life in healthy Dutch children. This study investigated a target cohort group of 1079 children forming part of the Generation R Study, a population-based prospective cohort study following children from fetal life until young adulthood, conducted in Rotterdam, The Netherlands. Nasopharyngeal swabs for M. catarrhalis culture were obtained at 1.5, 6 and 14 months of age, with all three swabs being available for analyses from 443 children. Data on risk factors possibly associated with M. catarrhalis colonization were obtained by questionnaire at 2, 6 and 12 months. M. catarrhalis colonization increased from 11.8% at age 1.5 months to 29.9% and 29.7% at 6 and 14 months, respectively. Two significantly important colonization risk factors were found: the presence of siblings and day-care attendance, which both increased the risk of being positive for M. catarrhalis colonization on two or more occasions within the first year of life. Colonization with M. catarrhalis was not associated with gender, educational level of the mother, maternal smoking, breast-feeding, or antibiotic use. Apparently, crowding is an important risk factor for early and frequent colonization with M. catarrhalis in the first year of life.