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In-vacuum undulators (IVU) are used extensively at light source facilities, in particular at medium-energy storage rings, where these devices are the main sources of high-brightness hard X-rays. The relatively small vertical magnetic gaps that are used in these planar undulators make them rather sensitive to misalignments of magnet arrays with respect to the electron orbit in the vertical plane. Based on commissioning results of undulator-based hard X-ray beamlines at the National Synchrotron Light Source II (NSLS-II)—a Department of Energy Office of Science User Facility at Brookhaven National Laboratory— IVU misalignment was found to be the most frequent cause of spectral “underperformance.” It is possible, nevertheless, to restore the performance using a spectrum-based IVU alignment procedure described in this article.