Despite their benefits, folate analogues can cause a range of side effects, some of which can be severe. Common side effects include myelosuppression (decreased production of blood cells), mucositis (inflammation of the mucous membranes), and gastrointestinal disturbances. Long-term use can also lead to liver and kidney toxicity. Patients undergoing treatment with folate analogues are often closely monitored to manage and mitigate these side effects.