Life cycle assessment is the predominant method to compare energy and environmental impacts of agricultural production systems. In this life cycle study, we focused on the comparison of swine manure to synthetic fertilizer as nutrients for corn production in Iowa. Deep pit (DP) and anaerobic lagoon (AL) treatment systems were compared separately, and urea ammonium nitrate (UAN) was chosen as the representative synthetic fertilizer. The two functional units used were fertilization of 1000 kg of corn in a continuous corn system and fertilization of a crop yielding 1000 kg of corn and a crop yielding 298 kg of soybean in a 2-yr corn-soybean rotation. Iowa-specific versions of emission factors and energy use were used when available and compared with Intergovernmental Panel on Climate Change values. Manure was lower than synthetic fertilizer for abiotic depletion and about equal with respect to eutrophication. Synthetic fertilizer was lower than manure for global warming potential (GWP) and acidification. The choice of allocation method and life cycle boundary were important in understanding the context of these results. In the DP system, methane (CH4) from housing was the largest contributor to the GWP, accounting for 60% of the total impact. When storage systems were compared, the DP system had 50% less GWP than the AL system. This comparison was due to reduction in CH4 emissions from the storage system and conservation of nitrogen. Nitrous oxide emissions were the biggest contributor to the GWP of UAN fertilization and the second biggest contributor to the GWP of manure. Monte Carlo and scenario analyses were used to test the robustness of the results and sensitivity to methodology and important impact factors. The available crop-land and associated plant nutrient needs in Iowa was compared with manure production for the current hog population. On a state-or county-wide level, there was generally an excess of available land. On a farm level, there is often an excess of manure, which necessitates long-distance transport.