Purpose: X-ray cone-beam CT (CBCT) is being increasingly used for various clinical applications, while its performance is still hindered by image artifacts. This work investigates a new source of reconstruction error, which is often overlooked in the current CBCT imaging. The authors find that the x-ray flat field intensity (I 0 ) varies significantly as the illumination volume size changes at different collimator settings. A wrong I 0 value leads to inaccurate CT numbers of reconstructed images as well as wrong scatter measurements in the CBCT research. Methods: The authors argue that the finite size of x-ray focal spot together with the detector glare effect cause the I 0 variation at different illumination sizes. Although the focal spot of commercial x-ray tubes typically has a nominal size of less than 1 mm, the off-focal-spot radiation covers an area of several millimeters on the tungsten target. Due to the large magnification factor from the field collimator to the detector, the penumbra effects of the collimator blades result in different I 0 values for different illumination field sizes. Detector glare further increases the variation, since one pencil beam of incident x-ray is scattered into an area of several centimeters on the detector. In this paper, the authors study these two effects by measuring the focal spot distribution with a pinhole assembly and the detector point spread function (PSF) with an edge-spread function method. The authors then derive a formula to estimate the I 0 value for different illumination field sizes, using the measured focal spot distribution and the detector PSF. Phantom studies are carried out to investigate the accuracy of scatter measurements and CT images with and without considering the I 0 variation effects. Results: On our tabletop system with a Varian Paxscan 4030CB flat-panel detector and a Varian RAD-94 x-ray tube as used on a clinical CBCT system, the focal spot distribution has a measured fullwidth-at-half-maximum (FWHM) of around 0.4 mm, while non-negligible off-focal-spot radiation is observed at a distance of over 2 mm from the center. The measured detector PSF has an FWHM of 0.510 mm, with a shape close to Gaussian. From these two distributions, the author calculate the estimated I 0 values at different collimator settings. The I 0 variation mainly comes from the focal spot effect. The estimation matches well with the measurements at different collimator widths in both horizontal and vertical directions, with an average error of less than 3%. Our method improves the accuracy of conventional scatter measurements, where the scatter is measured as the difference between fan-beam and cone-beam projections. On a uniform water cylinder phantom, more accurate I 0 suppresses the unfaithful high-frequency signals at the object boundaries of the measured scatter, and the SPR estimation error is reduced from 0.158 to 0.014. The proposed I 0 estimation also reduces the reconstruction error from about 20 HU on the Catphan c 600 phantom in the selected regions of interes...