The manure issue is complex and inherently interdisciplinary but, more fundamentally, it requires systems thinking. Current policies, technologies, infrastructure, incentives and modes of thinking about the problem fail to consider the system-wide implications, and thus fail to foster the creation of new and innovative solutions. At the farm level, complexity, uncertainty and lack of compatibility with the current farming system need to be addressed in order to promote better manure management. Production facilities, feed management and waste treatment systems (including centralized treatment plants) need to be designed to allow for beneficial use of manure components. At the industry level, changes in the poultry, swine and beef industries have resulted in concentration, both in terms of decision-making and geography. This currently limits the ability of these farmers to take a systems approach to livestock production. Environmental policies thus need to take account and advantage of this new reality. At the economy-wide level, factors affecting the demand and supply for alternative manure products need to be considered. A number of innovative uses are being developed in the private sector, but there are constraints as far as technology, institutions and infrastructure are concerned. A systems perspective will allow the design of policies and technologies that reduce environmental problems associated with manure, while promoting efficient utilization of the resource.