The aim of the study was to estimate the prevalence of asthma, allergic rhinitis/rhinoconjunctivitis and atopic eczema symptoms in rural and urban regions of Moldova. This study was performed regionally in geographically different parts of the country which differ in environmental conditions. The study was undertaken between January 2007 and May 2009 among the 7-16-year-old school children in 4 randomly selected villages with polluted drinking water (Anenii-Noi County and Hincesti County) and control region with relatively clean drinking water – village of Draguseni (Hincesti County), and two districts of the Chisinau city with varying degree of outdoor air pollution ranging from the highest pollution contents to relatively clean region. Data were collected using standardized ISAAC (International Study of Asthma and Allergy in Childhood) written questionnaire. A total of 1329 children participated in the study from the two age groups (under 10 years old and the older group). Results of the study showed that 38.7±1.3% of children answered affirmatively at least one question from the questionnaire regarding the presence of allergy symptoms at the studied population. Allergic symptoms are more frequent in polluted areas than in the clean ones with 43.0±1.6% and 29.0±2.2%, p<0.001, respectively. In younger group 40.0% of the children had symptoms of allergic diseases at some time in their life and in older group 38.2% of children, with a 1.7 folds higher incidence in adolescents living in polluted areas (43.7±2.0% and 26.0±2.6%, p<0,001 respectively). Estimated lifetime (ever) prevalence rates of symptoms were: wheezing 14.43% and 10.1%, allergic rhinitis symptoms 20.29% and 19.13%, and atopic dermatitis symptoms 12.22% and 15.0%, for younger and older age group respectively. In conclusion, allergic symptoms are frequently observed at school-age children, predominantly in adolescents, who live in unfriendly environmental settings. It is important to investigate the relationship between patterns found and environmental data to find out whether asthma and allergic disease increases are uniform and to identify factors that may relate to these increases.