Industrial control systems present security challenges, especially protocols that do not have security features and legacy systems that are often unpatched. Although the security of open standard protocols such as Modbus TCP has been extensively researched, relatively few efforts have focused on the security aspects of vendor-specific protocols and protocol extensions. These protocols, which also lack security measures like their standard counterparts, are used to configure and manage programmable logic controllers – they are, therefore, critical to the safe and secure operation of industrial control systems and the critical infrastructure assets they manage. Indeed, an adversary who exploits one of these protocols could perform actions such as starting and stopping programmable logic controllers, and modifying their configurations and their programs (i.e., their behavior).This paper analyzes the security of programmable logic controller configuration protocols. The comparative analysis leverages a testbed that includes programmable logic controllers from different manufacturers. The results include structured descriptions of feasible attacks and possible countermeasures.