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The prevalence of childhood eczema varies considerably between ethnic groups. However, data from longitudinal studies remain scarce.We examined the associations of ethnic origin with the development of eczema from birth until the age of 4 years, and whether known environmental and genetic risk factors explain these associations. This study was performed in a multiethnic population-based prospective cohort among 5,082 children. Ethnic origin was based on the parents' country of birth. Data on physician-diagnosed eczema were obtained by annual questionnaires. Information on environmental risk factors was mostly obtained by questionnaires. Filaggrin (FLG) mutations (2282del4, R2447X, R501X, and S3247X) were genotyped for 3,096 children. We used generalized estimating equation models to examine the associations of ethnic origin with the longitudinal odds of eczema at 6 months and 1, 2, 3, and 4 years of age overall and independently.Compared with Dutch children, Cape Verdean, Dutch Antillean, Surinamese-Creole, and Surinamese-Hindustani children had overall increased risks of eczema (OR (95%-CI): 1.53 (1.15, 2.03), 1.60 (1.21, 2.12), 1.95 (1.56, 2.44), and 2.06 (1.65, 2.57), respectively). Effect estimates for the associations of Cape Verdean and Dutch Antillean origin with eczema became non-significant after adjustment for genetic risk factors or both environmental and genetic risk factors, respectively. Surinamese-Creole and Surinamese-Hindustani children remained to have increased risks of eczema.Cape Verdean, Dutch Antillean, Surinamese-Creole, and Surinamese-Hindustani children had increased risks of eczema in the first 4 years of life. Environmental and genetic risk factors partly weakened these associations.