Cone-beam CT reconstruction can be performed at lower integral dose, by using a non-uniform beam filter between the x-ray source and the patient to obtain good image quality within an ROI with minimal artifacts. To evaluate the method, a human head phantom was placed on a rotary stage. Cone-beam projection images of the phantom were obtained with and without an ROI filter (dose reduction factor ~7). A mapping function was established to equalize the intensity outside the ROI (to compensate for the attenuation by the filter) to the intensity inside by assuming that those features lying both inside and outside very close to the edge of the ROI are the same. Reconstructed images were obtained using equalized projection images for 2 cases: one in which the outside region was smoothed using an averaging filter and the other with no smoothing outside. In addition, a third case was simulated by calculating the average pixel value inside the ROI for each image and assigning this value to all pixels outside the ROI for that image. The images were then back projected using a Feldkamp algorithm. We found that the three cases yield results inside the ROI comparable to those obtained using FFOV projections. In addition, the ROI filter reconstruction with smoothing provides image information outside the ROI comparable to the FFOV reconstruction. CT using an ROI filter provides a means to reconstruct reliable 3D for a volume of interest with greatly reduced integral dose compared to FFOV projections and with minimal artifacts.