Shear wave elastography (SWE) is a type of ultrasound elastography with which the elastic properties of breast tissues can be quantitatively assessed. The purpose of this study was to determine the impact of different regions of interest (ROI) and lesion size on the performance of SWE in differentiating malignant breast lesions. The study included 150 female patients with histopathologically confirmed malignant breast lesions. Minimal (Emin), mean (Emean), maximal (Emax) elastic modulus and elasticity ratio (e-ratio) values were measured using a circular ROI size of 2, 4 and 6 mm diameters and the lesions were divided into large (diameter ≥ 15 mm) and small (diameter < 15 mm). Highest Emin, Emean and e-ratio values and lowest variability were observed when using the 2 mm ROI. Emax values did not differ between different ROI sizes. Larger lesions had significantly higher Emean and Emax values, but there was no difference in e-ratio values between lesions of different sizes. In conclusion, when measuring the Emin, Emean and e-ratio of malignant breast lesions using SWE the smallest possible ROI size should be used regardless of lesion size. ROI size has no impact on Emax values while lesion size has no impact on e-ratio values.