If a patient suffers from frequent canker sores, there may be an underlying medical reason or illness present. See your medical doctor or dentist if there are any concerns that canker sores are frequent.nPredisposition to most canker sores may have a genetic cause. However, some diseases that affect the immune system may cause frequent or recurrent canker sores. These canker sore causing diseases include lupus, Crohn’s disease, celiac disease, or HIV/AIDS.nA medical doctor can order testing to determine a possible underlying medical reason for a patients’ frequent canker sores.