Security in the access to web contents and the interaction with web sites is becoming one of the most important issues in Internet. Servers need to provide certain levels of security so that the user feels comfortable when running the applications that provide the services he/she requires. HTTP over SSL is the most used solution, providing mutual authentication between the two interacting parts. The SSL protocol does not introduce complexity in web applications but increases the computational demand on the server, reducing its capacity to serve large number of clients and increasing the time to serve them. In order to compensate the degradation in the quality of service, the server needs to be upgraded with additional resources, mainly processors and memory. In this paper we analyze the scalability of servers that run secure dynamic web applications. We analyze how the server behaves when it is stressed with different number of clients and how the quality of service is degraded. We perform a detailed analysis of the server behavior and analyze the impact of adding more processors to the system that runs the server. The analysis is done using a fine-grained analysis framework that considers all levels in the application server execution (i.e. application, server, JVM and OS kernel). The RUBiS auction site benchmark is used to stress a Tomcat application server running on a commodity 4-way multiprocessor Intel platform with Linux.