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Agroforestry plantings and other trees intentionally established in rural and urban areas are emerging as innovative management options for addressing resource issues and achieving landscape-level goals. An understanding of the contributions from these and future plantings would provide critical information to policy and program developers, and a comprehensive inventory would contribute to estimating the cumulative effects of these plantings. Trees used in these practices are not explicitly inventoried by either of the two primary national natural resource inventories: the Forest Inventory and Analysis (FIA) program of the USDA Forest Service and the National Resources Inventory (NRI) of the USDA Natural Resources Conservation Service. The FIA program inventories trees in forests meeting specific size and density criteria. The NRI program compiles natural resource information on non-federal land in the United States. In this study, we estimate the agroforestry and other tree resources of Iowa and Missouri and document the obstacles to effective inventories of agroforestry practices. We propose minor modifications to national natural resource inventory programs that would lead to an improved assessment of agroforestry and other tree resources and practices.