Objectives To characterise the epidemiology of atopic eczema in adolescents from Kosovo, an area of very low prevalence of the condition and to know whether the same factors are associated to eczema with or without comorbid wheezing symptoms. Methods The cross-sectional survey Global Asthma Network validated questionnaire was self-completed by adolescents 13-14 years of age in the school setting from the main cities of Kosovo: Ferizaj, Gjakova, Gjilan, Peja, Prishtina and Prizren. Atopic eczema symptoms and diagnosis was put in relation with the environmental questionnaire which included questions on smoking; pet ownership; paracetamol use, truck traffic; siblings; time spent using screens or watching television; and exercise. Additionally, height and weight were measured at school. Results The prevalence of eczema symptoms ranged from 2.2% in Ferizaj to 5.5% in Gjakova. Severe symptoms were <1% in all cities. Eczema ever ranged from 3.0% in Ferizaj to 6.4% in Prizren. Factors significantly associated to the prevalence of current eczema symptoms in the metanalysis were male sex (pooled aOR 0.50; 95%CI 0.37-0.66); exercise (pooled aOR 2.79; 95%CI 1.89-4.10); and paracetamol intake (pooled 1.86; 95%CI 1.32-2.64). The corresponding figures for eczema ever were: 0.68 95%CI 0.44-1.06; 2.07 95%CI 1.48-2.90; and 1.19 95%CI 0.88-1.60. The associations tended to be higher in the subpopulation with eczema and wheeze comorbidity. Conclusions The prevalence of atopic eczema is very low in Kosovo and is associated to female sex, exercise, and paracetamol intake. Those associations are higher when eczema and wheezing are comorbid conditions.