In comparative life cycle assessments of agricultural production systems, analyses of both the trade-offs between environmental impacts and crop productivity and of the uncertainties specific to agriculture such as fluctuations in greenhouse gas (GHG) emissions and crop yields are crucial. However, these two issues are usually analyzed separately. In this paper, we present a framework to link trade-off and uncertainty analyses; correlated uncertainties are integrated into environment-productivity trade-off analyses. We compared three rice production systems in Japan: a system using a pelletized, nitrogen-concentrated organic fertilizer made from poultry manure using closed-air composting techniques (high-N system), a system using a conventional organic fertilizer made from poultry manure using open-air composting techniques (low-N system), and a system using a chemical compound fertilizer (conventional system). We focused on two important sources of uncertainties in paddy rice cultivation-methane emissions from paddy fields and crop yields. We found trade-offs between the conventional and high-N systems and the low-N system and the existence of positively correlated uncertainties in the conventional and high-N systems. We concluded that our framework is effective in recommending the high-N system compared with the low-N system, although the performance of the former is almost the same as the conventional system. (C) 2016 Elsevier B.V. All rights reserved.