The main focus of the cyber-security community has been to make operating systems and communication networks more secure and harder for attackers to penetrate. The most frequently used web application and user web pages are today developed with the Web Content Management System (WCMS), as it allows user-friendly access, easy development and operation. Any malware that can penetrate the WCMS can significantly affect the system itself and the service the web pages offer. This paper presents the approach for identifying the vulnerabilities of the majority of Internet sites with WCMS applications and the remedies to be applied with use of an automated, fast and dynamic vulnerability detection tool. The state of the web sites vulnerability in Europe and the impact factors that influence the vulnerability to be present are presented and discussed.