Sandhill Cranes (Antigone canadensis) of the midcontinent population (MCP) and Rocky Mountain population (RMP) are migratory game birds with stable populations that travel between Canada and the southern US and Mexico. In the winters of 2012–14, we performed gross and histologic examinations of 43 hunter-harvested Sandhill Cranes in Texas (MCP) and New Mexico (RMP) to assess the impact of disease on populations. Lesions were significantly more common in the MCP relative to the RMP, likely reflecting differential environmental exposure to pathogens and parasites. Grossly, liver nodules and esophageal granulomas were present in 8–39% of birds. In feces from over half of birds, we found coccidian oocysts with mitochondrial gene sequences identical to those of Eimeria gruis and Eimeria reichenowi previously obtained from sympatric Whooping Cranes (Grus americana). Over one-quarter of birds had liver and cardiac lesions suggestive of disseminated visceral coccidiosis. We documented proliferative colitis due to Cryptosporidium in a wild Sandhill Crane. Additionally, several endoparasites were found in histologic sections from several cranes, including a bird with respiratory trematodiasis and two birds with Tetrameres sp. in the proventriculus associated with ductal ectasia. In addition to describing lesions and parasites that impact Sandhill Crane health, these pathology data may also be relevant for the conservation of endangered Whooping Cranes using a surrogate species approach.