The present invention relates to a system for diagnosing Avellino corneal dystrophy, and more particularly to a system for diagnosing Avellino corneal dystrophy, in which whether a sample is normal or Avellino corneal dystrophy is determined based on the ratio of the input first PCR amplification value and the second PCR amplification value. The system makes it possible to diagnosis Avellino corneal dystrophy in a simpler and accurate manner without being influenced by the doctor's skill. Particularly, the inventive system makes the overall process systematic, and thus provides accurate diagnosis. In addition, the system can also easily administer a number of test subjects.