Methotrexate, a structural analogue of folic acid, is one of the most frequently used chemotherapeutics, especially in haematological malignancies, various solid tumours and also inflammatory disorders. Methotrexate interferes with folate metabolism, mainly by inhibition of dihydrofolate reductase, resulting in the suppression of purine and pyrimidine precursor synthesis. The depletion of nucleic acid precursors seems to be responsible for the cytostatic, cytotoxic and differentiation effects of methotrexate. Methylation of biomolecules represents another folate-dependent pathway that is also affected by methotrexate. Furthermore, methotrexate is able to modify metabolic pathways and cellular processes independently of folate metabolism. Based on the similar structure of methotrexate and of functional groups of certain histone deacetylase inhibitors, the ability of methotrexate to inhibit histone deacetylases was predicted and consequently verified. Recently published findings also suggest that methotrexate affects glyoxalase and antioxidant systems. Although methotrexate has been used as a folate metabolism antagonist in anticancer therapy for more than 60 years, the identification of its'other molecular targets in cellular metabolism still continues.