Purpose. High-quality medication reconciliation reduces medication discrepancies, but smaller hospitals serving rural patients may have difficulty implementing this because of limited resources. We sought to adapt and implement an evidence-based toolkit of best practices for medication reconciliation in smaller hospitals, evaluate the effect on unintentional medication discrepancies, and assess facilitators and barriers to implementation. Methods. We conducted a 2-year mentored-implementation quality improvement feasibility study in 3 Veterans Affairs (VA) hospitals serving rural patients. The primary outcome was unintentional medication discrepancies per medication per patient, determined by comparing the "gold standard" preadmission medication history to the documented preadmission medication list and admission and discharge orders. Results. In total, 797 patients were included; their average age was 68.7 years, 94.4% were male, and they were prescribed an average of 9.6 medications. Sites 2 and 3 implemented toolkit interventions, including clarifying roles among clinical personnel, educating providers on taking a best possible medication history, and hiring pharmacy professionals to obtain a best possible medication history and perform discharge medication reconciliation. Site 1 did not implement an intervention. Discrepancies improved in intervention patients compared with controls at Site 3 (adjusted incidence rate ratio [IRR], 0.55; 95% confidence interval [CI], 0.45-0.67) but increased in intervention patients compared with controls at Site 2 (adjusted IRR, 1.22; 95% CI, 1.08-1.36). Conclusions. An evidence-based toolkit for medication reconciliation adapted to the VA setting was adopted in 2 of 3 small, rural, resource-limited hospitals, resulting in both reduced and increased unintentional medication discrepancies. We highlight facilitators and barriers to implementing evidence-based medication reconciliation in smaller hospitals.