We evaluated ultrasonography (US) findings between benign and malignant phyllodes tumors and analyzed diagnostic performance of US-guided core needle biopsy (CNB) for phyllodes tumors. Surgically removed phyllodes tumors of 168 women were divided into two groups according to the benign and malignant (including borderline tumor) groups and 116 were benign and 52 were malignant. On US, the complex cystic echogenicity (p = 0.021), presence of cleft (p = 0.005) and higher final US assessment (p = 0.008) were more frequent in the malignant group. The sensitivity of CNB including fibroepithelial tumors was 67.9% (114/168) and the concordant rate between CNB and surgical excision was 82.1% (32/39) and 5.8% (3/52) in the benign and malignant group. Our results suggested that the US findings of complex cystic echogenicity, cleft, higher final US assessment were more frequent in malignant phyllodes tumors. The sensitivity of CNB was 67.9% (114/168) and malignant phyllodes tumors were rarely diagnosed as malignant by US-guided CNB.