Methotrexate (MTX) is still the gold standard in the treatment of rheumatoid arthritis and is used worldwide in more than 0.5 million patients with RA. Much hope is currently associated with the individualization of therapy provided to RA patients. The search is underway for biochemical and clinical markers that would be useful in predicting good response to MTX therapy. Along with clinical factors, genetic predisposition may also be helpful. Polymorphism of genes participating in MTX metabolism may affect the drug’s efficacy and the rate of adverse effects. Pharmacogenetic studies may contribute to more effective individualization of therapy for RA patients. There are many potential enzymes and transport proteins present in polymorphic forms, which are involved in transport of MTX into the cell, its metabolism and elimination from the cell. There is a chance that in the future through individualized therapy we will be able to customize therapy (type of drug, dose, route of administration) to the molecular subtype of the disease and the genotype of the patient. Patients with a specific type of polymorphism would require more frequent monitoring of the efficacy and safety of treatment. Note, however, that genetic predisposition is only one of the factors contributing to differences in pharmacotherapy in individual patients.