The measurement of modulation transfer functions (MTFs) in computed tomography (CT) is often performed by scanning a point source phantom such as a thin wire or a microbead. In these methods the region of interest (ROI) is generally placed on the scanned image to crop the point source response. The aim of the present study was to examine the effect of ROI size on MTF measurement, and to optimize the ROI size. Using a 4 multidetector-row CT, MTFs were measured by the wire and bead methods for three types of reconstruction kernels designated as 'smooth', 'standard', and 'edge-enhancement' kernels. The size of a square ROI was changed from 30 to 50 pixels (approximately 2.9 to 4.9 mm). The accuracies of the MTFs were evaluated using the verification method. The MTFs measured by the wire and bead methods were dependent on ROI size, particularly in MTF measurement for the 'edge-enhancement' kernel. MTF accuracy evaluated by the verification method changed with ROI size, and we were able to determine the optimum ROI size for each method (wire/bead) and for each kernel. Using these optimal ROI sizes, the MTF obtained by the wire method was in strong agreement with the MTF obtained by the bead method in each kernel. Our data demonstrate that the difficulties in obtaining accurate MTFs for some kernels such as edge-enhancement can be overcome by incorporating the verification method into the wire and bead methods, allowing optimization of the ROI size to accurately determine the MTF.