PurposeOpen surgical muscle biopsy (OB) and percutaneous Bergstroem needle muscle biopsy (NB) are equally accepted procedures. However, there are no data comparing intraprocedural pain for both techniques. We designed this prospective trial to test the hypothesis that the less invasive NB causes less intraprocedural pain than OB.MethodsIn a two-center prospective trial, 33 patients underwent both procedures in one session. All patients quantified intraprocedural pain using the numeric rating scale (NRS). Mean NRS values were calculated along with the difference in NRS values (ΔNRS) between both types of biopsies.ResultsMean NRS values were 4.5 (±2.7 standard deviation [SD]) for NB and 3.2 (±2.1) for OB (P=0.02). Of the patients, 57.6% described the ΔNRS as ≤2 NRS points. Regarding the pain categories “mild” (NRS 0–3), “moderate” (NRS 4–7), and “severe” (NRS 8–10), no significant difference was observed between NB and OB. Patients who found NB to be more uncomfortable were more likely to quantify the ΔNRS as >2 NRS points than patients finding OB more uncomfortable.ConclusionOur results do not support the hypothesis that intraprocedural pain in NB is less than in OB. When informing the patient about both types of muscle biopsies, the amount of intraprocedural pain should not serve as a differentiating characteristic.