The purpose of Building Automation Systems (BAS) is to centralise the management of a wide range of building services, through the use of integrated protocol and communication media. Through the use of IP-based communication and encapsulated protocols, BAS are increasingly being connected to corporate networks and also being remotely accessed for management purposes, both for convenience and emergency purposes. These protocols, however, were not designed with security as a primary requirement, thus the majority of systems operate with sub-standard or non-existent security implementations, relying on security through obscurity. Research has been undertaken into addressing the shortfalls of security implementations in BAS, however defining the threats against BAS, and detection of these threats is an area that is particularly lacking. This paper presents an overview of the current security measures in BAS, outlining key issues, and methods that can be improved to protect cyber physical systems against the increasing threat of cyber terrorism and hacktivism. Future research aims to further evaluate and improve the detection systems used in BAS through first defining the threats and then applying and evaluating machine learning algorithms for traffic classification and IDS profiling capable of operating on resource constrained BAS.