As organizations become more and more process-centered and as the extended enterprise becomes more of a reality, there is an increasing need to move towards the intelligent enterprise characterized by its agility for provisioning resources and services and the adaptation and optimization of its business processes. Many are the challenges that need to be faced to equip the extended enterprise with intelligence, in particular with business process intelligence. In this paper we present an overview of some challenges, opportunities and directions for analysis and optimization of business processes towards the intelligent enterprise.