The primary goal of this paper is to analyze the quality of Website design of various Websites of universities in India and identifying the causes that affect the quality of Website design. The Website of each university is scanned using W3C guidelines which are the bases for any type of Web application. The parameters such as Web page size, down loading time, broken links, Web page errors etc., are considered in identifying the qualitative measures for Website design. Different kinds of tools are used to examine the components of Websites of various Indian Universities. These tools include: W3C Link checker, W3C Markup Validation Service, Webpage Analyzer and Website Extractor. The W3C Link checker accepts URL address of Web page and parses each and every hyperlink to find broken links in the page. The W3C Markup Validation Service finds the errors regarding HTML tags usage errors, properties of Web page and standards of the Web page mentioned by W3C Consortium. The Webpage Analyzer finds the number of objects used in each Web page, Web page size, downloading time etc., The Website Extractor extracts URL addresses of all Web pages of the Website.