Veterans have a profound degree of vitamin D deficiency that may contribute to adverse health outcomes. Some veterans, especially African Americans at high risk of vitamin D deficiency, may not be receiving appropriate attention. We hypothesized variations in vitamin D status and monitoring across six different VAMCs and that these differences are associated with health care costs. A retrospective analysis of the medical data in the Veterans Integrated Service Network 9 (Southeastern United States) was performed, yielding a sample of 15,340 veterans. Monitoring of vitamin D, vitamin D levels, and medical costs and services in all categories varied greatly by site. Memphis tested vitamin D levels less often despite the increased minority presence and high levels of deficiency. Vitamin D deficiency and lack of monitoring predicted increased inpatient health care costs at all sites, but did not fully account for site-cost variations in controlled analyses. Vitamin D deficiency remains a significant problem among veterans in the Southeastern United States and is closely linked to increased health care costs. We recommend protocols that recognize site differences and facilitate testing and monitoring of vitamin D levels, especially in high-risk groups of veterans.