TPMT is an enzyme that catalyses S-methylation of thiopurine drugs, which activity is genetically determined. TPMT-deficient patients are at risk of toxicity after standard doses of thiopurine drugs. We describe a case of Crohn’s disease diagnosed patient inheriting genetic TPMT deficiency (TPMT*3A/*3A genotype), who developed severe aplastic anaemia, confirmed by biopsy, after 55 days of treatment with AZA at a standard daily dose of 2.5 mg/kg. This case demonstrates the importance of TPMT polymorphism testing in order to prevent myelotoxicity during treatment with thiopurine drugs.