We conducted diagnostic investigations to analyze the causes of abortions (46 cases, 65.7%), deaths (22 cases, 31.4%) and muscular lesions (2 cases, 2.9%) occurred after foot and mouth disease (FMD) vaccination in livestock farms in Korea. Bacterial culture, enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) were performed to detect the causative agents of abortion in bovine and caprine. The diagnostic results showed that 36 (51.4%) cases, referring as “Identified”, were occurred by influence of underlying disease including bovine viral diarrhea (12 cases, 17.1%), neosporosis (7 cases, 10.0%), septicemic colibacillosis (5 cases, 7.1%), Q fever (4 cases, 5.7%) and other abnormal conditions (8 cases, 11.4%) not by vaccination. Other 2 (3.0%) cases were suspected to be vaccine-associated adverse reaction on the basis of pathological findings (shock lung, oil-component-induced granuloma) and clinical symptoms (dyspnea with pulmonary edema). The other 32 (45.7%) cases were determined “Unknown” because any pathogens and pathological changes were not identified. However, many of the “Unknown” cases were presumptive to be the vaccine-related adverse reaction based on epidemiological investigation, especially, the cases which showed the clinical signs within 2 days after the vaccination. It is important to conduct pathological, microbilogical and epidemiological investigation to diagnose whether the cases are from vaccine-associated adverse reaction or not.