Crohn's disease (CD) and ulcerative colitis (UC) are the most proeminent forms of inflammatory bowel diseases (IBDs). Azathioprine (AZA) is the most common drug used to maintain clinical remission in IBDs. However, the treatment with AZA leads to some drug side effects. Gene polymorphism of thiopurine S-methyltransferase (TPMT) correlates with decreased enzyme activity, which causes an increase in the incidence of these side effects. In addition, the association of AZA with some drugs might modify the final levels of active metabolites. The aim of this study was to investigate the impact of polymorphisms in TPMT gene as well as the interactions by the association of AZA with other drugs in IBD treatment. We studied 90 patients (CD = 53 and UC = 37). Quantitative analysis of AZA metabolites has performed by High Performance Liquid Chromatography-UV. The TPMT gene polymorphisms have evaluated by Polymerase Chain Reaction/Fragment Length Polymorphism. AZA+ infliximab group has shown the highest percentage of patients with 6-TGNt toxic levels (13.3%) and AZA+ mesalazine group has presented the highest percentage of patients with therapeutic levels (16%). The presence for each genotypes variation was demonstrated as follows: TPMT*1 (87.8%), TPMT*2 (1.1%), TPMT*3A (1.1%), TPMT*3B (5.6%) and TPMT*3C (4.4%). In our study, the metabolism of azathioprine was influenced by non-genetic factors. These factors were resulted of drug interactions caused by associations in IBD treatment. Polymorphisms detected in this study did not demonstrate negative effect on levels of metabolites.