BACKGROUND: Variability in the prevalence of allergic diseases has been detected not only between different countries, but also between cities with similar national and different socio-economic or climatic characteristics. The aim of this study was to determine the prevalence of childhood asthma and allergies and which factors are associated with them, in the two largest Greek cities, Athens and Thessaloniki. METHODS: Two thousand and twenty-three Greek 9-10-year-old schoolchildren from Athens (Central Greece) and Thessaloniki (North Greece, more humid), were included in ISAAC-II study. All participants followed the ISAAC-II protocol by questionnaire, skin prick testing and flexural dermatitis examination. RESULTS: Compared with Athens, the prevalence of current wheezing (8.4% vs. 5.7%, p=0.002), lifetime asthma (11.5% vs. 7.7%, p=0.004), atopic current asthma (3.2% vs. 1.6%, p=0.02), allergic rhinitis (8.2% vs. 5.2%, p=0.007), and hay fever (21.7% vs. 12.5%, p<0.001) were higher in Thessaloniki. The overall sensitisation rate was also higher in Thessaloniki than in Athens (25.2% vs. 16%, p<0.001) with more prevalent sensitising due to the perennial allergens (D. pteronyssinus, D. farinae, Alternaria tenuis) and cat dander. Perennial allergens sensitisation was a risk factor for current asthma in both cities. CONCLUSION: A higher prevalence of asthma symptoms, allergic rhinitis, and sensitisation rate was detected in Greek schoolchildren living in Thessaloniki compared to those in Athens. Allergy to mites and mould was more prevalent in Thessaloniki. The more humid weather of Thessaloniki may be implicated.