The last decade has seen an unprecedented rate of development of Web-Based Information System (WBIS). Enormous investment is currently being made in WBIS systems. There is a concern about whether the true capability of WBIS is being realized. As a consequence, growing attention is being paid to assessing the inherent contribution of WBIS. In this paper, we propose a WBIS audit methodology. The latter has two main features: 1) it structures the audit process as a hierarchical evaluation tree, using an Analytic Hierarchy Process model, 2) it allows the evaluation of a WBIS according to a specific set of criteria based on quality, security and readability requirements. Unlike past approaches, our methodology allows independent auditors, companies and users to minimize the time and effort needed to evaluate WBIS. It has been applied to a real-life example which is described in the paper, allowing us to validate our WBIS audit approach.