This paper deals with the problem of securing the configuration phase of an Internet of Things ( IoT) system. The main drawbacks of current approaches are the focus on specific techniques and methods, and the lack of a cross layer vision of the problem. In a smart environment, each IoT device has limited resources and is often battery operated with limited capabilities ( e. g., no keyboard). As a consequence, network security must be carefully analyzed in order to prevent security and privacy issues. In this paper, we will analyze the IoT threats, we will propose a security framework for the device initialization and we will show how physical layer security can effectively boost the security of IoT systems.