Atopic eczema (AE) is the most common childhood inflammatory skin condition. The aim of this study was to evaluate the prevalence of AE and its relation to various risk factors. In a cross-sectional study, 9,991 children ages 13 to 14 years in 61 primary schools in 32 districts of Istanbul were evaluated. The prevalence of AE and associated symptoms was assessed using the International Study of Asthma and Allergies in Childhood protocol. The relationship between risk factors and AE was evaluated using multivariate logistic regression analysis. Ten thousand nine hundred eighty-four questionnaires were distributed to 13- and 14-year-old children in 61 schools in 32 districts of Istanbul, 9,991 of which were suitable for analysis, for an overall response rate of 91.7%. There were 4,746 boys (47.9%) and 5,166 girls (52.1%) (M/F ratio 0.920). The rates of itchy rash ever, 12-month itchy rash, and doctor-diagnosed AE ever were 18.2%, 12.0%, and 2.8%, respectively. The difference between rates for itchy rash ever, 12-month itchy rash and doctor-diagnosed AE was high (12.8–31.3, 5.8–24.8, and 0–17.2, respectively) between the districts of Istanbul. Female sex, AE family history, watching television more than 5 hours a day, region of the district, and tonsillectomy history were found to be significantly associated with doctor-diagnosed AE at p < 0.05 in multivariate analysis. This study found a low prevalence of doctor-diagnosed AE and related symptoms in Istanbul. Several risk factors were found to be associated with doctor-diagnosed AE.