Web-Based instruction (WBI) has been a main stream of recent reforms in higher education. However, most college instructors do not agree with others in the ways of implementing and designing WBI. The variation is significant in the administration of academic affairs, the technology literacy levels of both instructors and students, the infrastructure of campus networking, and the amounts of financial investment. The results of WBI implementation are therefore diversified. Some are acceptable while some are unbearable. The key to success or failure of WBI is in the hand of accreditation. This paper first reviewed the accreditation mechanism in other countries, and found that there are two different WBI accreditations: institute accreditation and courseware accreditation. Taiwan government had invited scholars and experts to conduct a series research on the issue of WBI accreditation. They proposed three sets of accreditation indicators for Content accreditation, Course accreditation, and Institute accreditation. In 2006, Taiwan established the Accreditation Center for E-learning (ACE) based on suggestions of the previous research. The author is appointed to lead the ACE management team for the first 18 months. To systematically assess the applications for Content accreditation, Course accreditation, and Continuing graduate Programs, ACE team has carefully defined application procedures, work flows, and evaluation criteria. In this paper, the author also reported the accreditation results at the end of 2006.