Asthma and atopic dermatitis share several common features and Cysteinyl-leukotrienes are mediators that participate in the pathogenesis of both diseases. Recently, a new polymorphism (927T>C) has been identified in cysteinyl-leukotriene type-1 receptor (CYSLTR1) gene. This gene is found on the X chromosome. The aim of this study was to analyze this SNP in a population of children with asthma and atopic dermatitis. In this study, 166 individuals, 79 adult controls (CTR) and 87 children with asthma (AA) were included. Forty-one patients with asthma presented atopic dermatitis (AA-AD). Adults were chosen as controls to confirm lack of development of asthma and allergy during childhood. Standardized history, physical examination, skin prick tests, and lung function measurements were performed in all patients. The 927T>C CYSLTR1 SNP was analyzed by direct sequencing after PCR amplification. In males (53 individuals), the C allele was significantly more common among AA-AD patients (47%) than in CTR (8%) (Fisher's p < 0.005; Monte Carlo p < 0.008; OR:9.78; 95%CI: 1.73–55.30). When comparing AA-AD vs. AA-NAD (patients with asthma but not atopic dermatitis), significant differences were observed, (47% vs. 15%, Fisher's p = 0.014; Monte Carlo p = 0.022; OR: 4.97; 95%CI: 1.29–19.13). No differences in allele distribution were observed between these disease sub-groups in females. The 927T>C is a silent SNP; however, it could affect transcription or translation or may be linked to an unidentified, functional polymorphism and thus may pre-dispose male children to asthma and atopic dermatitis in our population. Further studies are needed to confirm these findings.