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Abstract Background The use of two-dimensional (2D) ultrasound for guiding radiofrequency ablation (RFA) of benign thyroid nodules presents limitations, including the inability to monitor the entire treatment volume and operator dependency in electrode positioning. We compared three-dimensional (3D)-guided RFA using a matrix ultrasound transducer with conventional 2D-ultrasound guidance in an anthropomorphic thyroid nodule phantom incorporated additionally with temperature-sensitive albumin. Methods Twenty-four phantoms with 48 nodules were constructed and ablated by an experienced radiologist using either 2D- or 3D-ultrasound guidance. Postablation T2-weighted magnetic resonance imaging scans were acquired to determine the final ablation temperature distribution in the phantoms. These were used to analyze ablation parameters, such as the nodule ablation percentage. Further, additional procedure parameters, such as dominant/non-dominant hand use, were recorded. Results Nonsignificant trends towards lower ablated volumes for both within (74.4 ± 9.1% (median ± interquartile range) versus 78.8 ± 11.8%) and outside of the nodule (0.35 ± 0.18 mL versus 0.45 ± 0.46 mL), along with lower variances in performance, were noted for the 3D-guided ablation. For the total ablation percentage, 2D-guided dominant hand ablation performed better than 2D-guided non-dominant hand ablation (81.0% versus 73.2%, p = 0.045), while there was no significant effect in the hand comparison for 3D-guided ablation. Conclusion 3D-ultrasound-guided RFA showed no significantly different results compared to 2D guidance, while 3D ultrasound showed a reduced variance in RFA. A significant reduction in operator-ablating hand dependence was observed when using 3D guidance. Further research into the use of 3D ultrasound for RFA is warranted. Relevance statement Using 3D ultrasound for thyroid nodule RFA could improve the clinical outcome. A platform that creates 3D data could be used for thyroid diagnosis, therapy planning, and navigational tools. Key Points Twenty-four in-house-developed thyroid nodule phantoms with 48 nodules were constructed. RFA was performed under 2D- or 3D-ultrasound guidance. 3D- and 2D ultrasound-guided RFAs showed comparable performance. Real-time dual-plane imaging may offer an improved overview of the ablation zone and aid electrode positioning. Dominant and non-dominant hand 3D-ultrasound-guided RFA outcomes were comparable. Graphical Abstract