Gene expression was analyzed in 368 samples, RNA was hybridized on the whole genome chips with 48 thousand genes/chip. Samples were evaluated according to disease and locality (Ostrava–asthma, Ostrava–control, Prachatice-asthma, Prachatice-control). Differences in gene expression were checked by t-test and ANOVA. When children are compared according to locality and the change in the gene expression >1.5, we observed 64 deregulated genes ( Fig. 5). When we compare Ostrava-asthma vs. Ostrava-control, we observed 12 deregulated genes, in Prachatice 17 deregulated genes. Using Venns’ diagrams, genes specific for asthma in Ostrava and asthma in Prachatice completely differ, no one gene was observed in both localities ( Fig. 6). In Ostrava, MAPK signaling pathway (p < 0.01, 1.5-fold) and in Prachatice cytokine-cytokine receptor interaction pathway (p < 0.01, 1.5-fold) were affected.