This study concerns DB quality of the Web databases which has been produced in medical science. For the quality evaluation of Embase and PubMed, 10 evaluating criteria were developed on the basis of literature review. The evaluation result showed that PubMed has superiority to the currentness, accuracy, completness, consistency, ease of use, customer support, searchability, cost, and network & H/W on DB, but Embase has only superiority to the coverage. It is needed for purchasing, user training, and library service based on the above evaluation result.