Dioxins such as dioxin and dibenzofuran are compounds having acute and chronic toxicity. The interaction between nucleobase and dioxin was analyzed by molecular orbital calculation. Model molecules are used for nucleobases such as adenine, cytosine, guanine, thymine, and uracil, and the dioxins are calculated for four compounds including two dioxins and two dibenzofurans with a large toxicity equivalence factor. MP2 calculation was performed for the optimized structure obtained by the HF calculation, and the stabilization energy was obtained. At that time, BSSE was corrected. A stable structure of nucleobase and dioxin was obtained. The stabilization energy of nucleobase and dioxin was less than about half that of Watson-Crick base, but the results suggest the possibility that nucleobase and dioxin form hydrogen bonds.