OBJECTIVE: To evaluate the diagnostic performance of fine needle aspiration (FNA) and core needle biopsy (CNB) in patients with anaplastic thyroid cancer (ATC) or thyroid lymphoma (TL). METHODS: Between January 2000 and March 2012, 104 patients were diagnosed with ATC or TL by means of ultrasound (US)-guided FNA, CNB, or surgery. This study ultimately included 99 patients with ATC (n = 59) or TL (n = 40). We evaluated the sensitivity and positive predictive value of FNA and CNB for the diagnosis of ATC and TL, and compared the rates of diagnostic surgery between FNA and CNB. RESULTS: FNA was used in 83 patients, and CNB was used in 32 patients initially (n = 16), after FNA results (n = 8), or simultaneously with FNA (n = 8). CNB achieved sensitivity of 87.5 % (28/32) and positive predictive value of 100.0 % (28/28) for the diagnosis of ATC and TL. The respective values for FNA were 50.6 % (40/79) and 90.9 % (40/44). The rate of diagnostic surgery was significantly lower after CNB (4/32, 12.5 %) than after FNA (28/79, 35.4 %) (p = 0.020). CONCLUSIONS: CNB was able to reduce unnecessary diagnostic surgery in patients with ATC or TL by virtue of its superior diagnostic sensitivity and positive predictive value compared to FNA. KEY POINTS: * Diagnostic sensitivity and PPV for CNB were 87.5 % and 100.0 %, respectively. * The respective values for FNA were 50.6 % and 91.0 % for ATC and TL. * Diagnostic surgery rates were reduced after CNB compared to FNA (p = 0.020).