The aim of this study was to determine whether SNP in filaggrin gene and expression of filaggrin mRNA in buccal epithelium are associated with childhood eczema and with the phenotype of childhood eczema combined with asthma. Genotyping for FLG (rs11204981) was performed in the following populations: patients with asthma (n = 99); ages 5-18 years (8 ± 2.1), and control group (n = 98); ages 5–18 years (12 ± 2.1) by using Real-time PCR. Level of mRNA expression was estimated by using reverse transcription and following real-time PCR. It was found out that 5.05 % of patients and 2.02 % of control group had minor allele (AA; P>0.05), 27.27 % and 36.36 % of patients and control group, respectively, had heterozygous allele (GA; P>0.05) and 67.68 % and 61.62 % had major allele (GG) (P>0.05). Variants with the AA-genotype of the FLG rs11204981 were found to be 2.5 times more frequently among patients than in control group. We also found out that the level of mRNA FLG expression in GG-genotype is 22.8 ± 11.67 (P>0.05 compared to AA-genotype), 92.95 ± 35.3 in GA genotype (P<0.05compared to GG-genotype) and 21.8 ± 13.4 in AA genotype (P>0.05 compared to GA-genotype). Thus, heterozygous variant has significantly higher expression of filaggrin in buccal epithelium. We suggest that SNP in FLG (rs11204981) may serve as an important predictive marker for the combined eczema plus asthma phenotype, and that the highest level of expression in heterozygous may have a protective role in developing allergy phenotype.