The X-ray test is a simple, fast, non-destructive, and highly precise test that enables detailed examination of internal seed morphology and identification of seed damage and its location and type. The objective of the present study was to evaluate the efficiency of the X-ray test and the relationship between the structure of Crotalaria junceaseeds and germination. Six lots of Crotalaria junceaseeds of the IAC-KR1 cultivar were subjected to X-ray and germination tests. Normal and abnormal seedlings and dead seeds were photographed and analyzed together with the X-ray images of the seeds. Results showed that analysis of X-ray images is effective in identifying mechanical damage, stink bug damage, and deteriorated tissues in Crotalaria junceaseeds and is able to establish an association between their occurrence and germination.