We examined the low contrast resolution of cone beam CT (CBCT) equipped with an indirect-type flat panel detector and compared it with a commercial CT unit (Robusto). In CBCT, the X-ray tube voltage of 110 kV was used, and in the Robusto, the usual 120 kV was used for examinations. The computed tomography dose index (CTDI) of the two systems was measured, and images scanned at about the same exposure to radiation were compared. The modulation transfer factors of the two systems were measured, and the convolution kernel that was the nearest to the characteristic of CBCT was chosen among kernels of the Robusto. A water phantom with a diameter of 200 mm was scanned, Wiener spectra were calculated, and signal-to-noise ratios were compared. The low contrast resolution phantom was scanned, and detectability and contrast-to-noise ratio (CNR) were measured. In addition, we placed diluted contrast medium into a phantom, scanned the phantom, and measured the detectability and CNR. When the X-ray irradiation condition of CBCT was 75 mAs at 110 kV, the equal dose of radioactivity in the Robusto was 50 mAs at 120 kV. In the low contrast resolution phantom, detectability was 8.7%mm in CBCT, and 9.4%mm in the Robusto. In the low contrast resolution evaluation phantom, CNR was 1.39 in CBCT, and 2.69 in the Robusto. With diluted contrast medium, CNR was 1.28 in CBCT, and 0.60 in the Robusto. CBCT was inferior to the Robusto in a low contrast resolution phantom, but CBCT was superior to the Robusto using diluted contrast medium. We found that CBCT was useful in examinations using contrast media.