The receptor's protein, interleukin-23 (IL-23), maintains chronic inflammation and fights bacterial infections.
The Science Express study researchers say the results could aid in developing new drugs.
Inflammatory bowel diseases are predisposed to families and scientists have been guessing that it had a genetic component.
The researchers used a genome-wide study of more than 1,000 people suffering from Crohn's disease and those without. They looked for variations of the DNA sequence that could link to the inflammatory bowel disease.
Three variations were found with two being already known, and one being new.
The new variation seen in the IL-23 receptor was more likely to occur in people without the disease than those with it.
Dr Judy Cho, one of the authors from the Department of Medicine and Genetics at Yale University, said: "We appear to have identified a gene variant that protects against development of IBD."
"It causes us to think about the genetics of health as well as the genetics of the disease."
"One mutation appears to offer significant protection from IBD, and will be a crucial target for drugs that might better manage Crohn's disease and ulcerative colitis."
One of participants of the research, Professor Christopher Mathew, said the work in Science suggested the IL-23 gene played a "key role" in the inflammatory response.


