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The lymphotoxin-α (LT-α) gene is located on chromosome 6 (6p21.1–6p21.3) and it may regulate tumor necrosis factor (TNF) production. TNF is a potent cytokine in the airway inflammatory response. Polymorphisms of TNF-associated genes have been related to asthma. This study investigated an LT-α-NcoI polymorphism in the first intron of the LT-α gene (LT-α-NcoI*1 allele, as a variant type; and LT-α-NcoI*2 allele), which may predispose individuals to asthma and atopy. Methods: Polymerase chain reaction-based assays were performed to determine LT-α-NcoI genotypes among our subjects. A genetic case control analysis was then performed on 114 atopic asthmatic and 155 non-asthmatic unrelated children. Results: There was a statistically higher frequency of LT-α-NcoI*1 allele carriers (1/1 + 1/2) in the subjects with atopic asthma than in controls (OR = 1.923; 95% CI = 1.061–3.484; p = 0.031). Conclusion: The results indicate that LT-α-NcoI*1 may be a risk factor for atopic asthma in Taiwanese children.