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 (MPNs), 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.