Asthma and allergic rhinitis are common problems in children and the causative pollen allergens vary according to the geographical area. The aim of this study was to investigate patterns of sensitization to common inhalant allergens, especially pollens, in Turkish children living in the Trakya region and to determine differences between rural and urban areas. Allergen skin testing was prospectively performed on 539 children aged between 4 and 17 years with respiratory allergy. The reaction was considered to be positive if the mean wheal diameter was at least 3 mm greater than that of the negative controls. We detected positive skin reactions in 420 (77.9%) children. Two hundred and eighty-one (52.1%) mite, 277 (51.4%) pollen, 174 (32.3%) mold, 65 (12.1%) animal dander, 12 (2.2%) cockroach and 6 (1.1%) latex skin sensitivities were detected. Among the pollen allergies 173 were cereal pollen (32.1%), 170 grass pollen (31.5%) and 144 tree pollen allergies (26.7%). The most common positive skin test among the pollens was to cultivated wheat (Titicum vulgare) (n = 116, 21,5%), followed by rye grass (Lolium perenne) and orchard grass (Dactylis glomerata). Positive skin reactions to Alternaria, to Candida albicans, and to all pollens except Ulmus competris, Pinus sylvetris, Platanus vulgaris and Tilia platyphyllos, were higher in children with allergic rhinitis than in those with asthma. In children from rural areas, allergic skin reactivity was found to be more common against Candida albicans, sheep dander and all pollens except Corylus avellana, Fraxinus excelsior, Populus alba, Pinus sylvetris, Platanus vulgaris and Chenopodium album, than in urban children. Although Trakya is close to Greece and other Mediterranean countries, this study suggests that the pollens, which sensitize children, are not similar.