Crohn's disease is inflammatory bowel disease characterized by excessive inflammatory response that affects the full thickness of intestinal wall and skip lesions of the intestinal tract. Mucosal healing or deep remission, means mucosa with no signs of inflammation or ulcerations. Endoscopic procedures are crucial in the assessment of mucosal healing but there are still no exact criteria for defining mucosal healing. It is associated with fewer hospitalisations and surgeries in patients and a more favorable disease course of the disease. Azathioprine has a long tradition of use in the treatment of Crohn's disease, and the guidelines recommend it as a drug for the maintenance of remission in patients with moderate to severe disease. To optimize azathioprine treatment, methods for measuring the concentrations of its metabolites and genotyping thiopurine methyltransferase are used, which allow more precise drug dosing and safer patient selection. The first studies noticing the occurrence of mucosal healing in patients treated with azathioprine were published in the 1990s, and research on the role of azathioprine in mucosal healing continues to this day. According to the results of previous studies, the prevalence of mucosal healing in patients treated with azathioprine ranged from 16.5 to 83%, which indicates large differences in design between studies. Azathioprine has been shown to be a relatively successful drug for achieving mucosal healing in patients who tolerate it and who have started taking it earlier in the course of the disease. Its benefit in combination with anti-TNF antibodies has also been proven in reducing the immunogenicity of the biological molecule and consequently achievement of the higher serum drug concentrations, which ultimately enhances mucosal healing. Previous research focused on the achievement of mucosal healing using azathioprine lacks an individualized approach to the patient in drug dosing and a standardized approach to patient monitoring. Additional research is needed to apply these strategies, which could ultimately lead to treatment optimization that could possibly include a higher prevalence of mucosal healing.