Present aircraft are highly automated systems. In general, automation improved aviation safety significantly. However, automation exhibits itself in many forms of adverse behaviors related to human factors problems. A major finding is that insufficient support of partnership between the pilot crew and the aircraft automation can result in conflicting intentions. The European project A-PiMod (Applying Pilot Models for Safer Aircraft) addresses issues of conventional automation in the aviation domain. The overall objective of the project is to foster pilot crew-automation partnership on the basis of a novel architecture for cooperative automation. An essential part of the architecture is an intention recognition module. The intention recognition module employs a Hidden Markov Model (HMM) to infer the most probable current intention of the human pilots. The HMM is trained and evaluated with data containing interactions of human pilots with the aircraft cockpit systems. The data was obtained during experiments with human pilots in a flight simulator.