Azathioprine is primarily used as an immunosuppressive agent in organ transplantation to prevent rejection of transplanted organs such as kidneys, liver, and heart. It works by inhibiting the proliferation of immune cells, thereby reducing the immune system's ability to attack the transplanted organ.

In addition to its use in transplantation, it is also employed in the treatment of autoimmune diseases. For conditions like rheumatoid arthritis, it helps to control the overactive immune response that causes inflammation and joint damage. Similarly, it is used in managing systemic lupus erythematosus to alleviate symptoms by suppressing the immune system's abnormal activity.

Azathioprine is also effective in treating inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. It helps to reduce inflammation in the gastrointestinal tract, leading to symptom relief and improved quality of life for patients.

Furthermore, it is sometimes prescribed for certain cases of severe psoriasis and autoimmune hepatitis, where it helps to modulate the immune response and reduce disease progression.

Due to its immunosuppressive properties, patients on Azathioprine require regular monitoring for potential side effects, such as increased susceptibility to infections and bone marrow suppression.