Electron-beam probe shape is typically determined by imaging a known or quasirandom target; however, neither standard targets nor two-dimensional image acquisition and processing are suitable for real-time probe characterization during lithographic exposures. Here a new technique for continuously monitoring probe shape is proposed and evaluated. Fourier analysis of the signal generated by an in situ fiducial grid allows estimation of the x and y widths and rotation of a Gaussian beam. The grid itself is rotated with respect to the beam deflection axes to allow real-time estimation of two-dimensional probe shape from a one-dimensional line scan across the grid. Monte Carlo simulations of beam parameter variances versus signal-to-noise ratio reveal regions of operation where the algorithm’s precision is limited by either noise or grid geometry. Experiments using a 1μm period grid to estimate probe shape as a function of defocus demonstrate the effectiveness of the new approach.