Abstract Objective In an era of controversy in regard to ‘hydroxyurea‐leukaemogenicity’ and when interferon‐alfa2 ( IFN ) is being revived in the treatment of Philadelphia‐negative myeloproliferative neoplasms ( MPN s), we aim in this single‐centre observational study to describe the frequencies of second malignancies in a cohort of MPN patients treated with hydroxyurea ( HU ) or IFN monotherapy or the combination of these agents. Patients and methods Records of a MPN cohort of 196 patients were reviewed, and a retrospective analysis was performed on 90 patients treated with HU , 38 patients treated with IFN and 68 patients treated with both IFN and HU . Logistic regression was used to compare frequencies in second malignancies. Results Patients treated with HU had a significantly higher risk of developing all second malignancies compared with patients treated with IFN [ HU vs. IFN : OR of 4.01 (95% CI : 1.12–14.27, P ‐value: 0.023) and HU ‐ IFN vs. IFN : OR 5.58 (95% CI : 1.55–20.15, P ‐value: 0.004)]. Conclusion We have found an increased risk of second malignancies in MPN patients treated with HU compared with patients treated with IFN .