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Purpose: The relationship between eye movements and the visual evoked potential (VEP) response was examined in two subjects with infantile nystagmus syndrome (INS). Changes in VEP amplitude were compared between periods of foveation versus periods of high-frequency nystagmus. An analysis is proposed that improves extraction of the checkerboard reversal VEP signal from subjects with INS. Methods: INS subjects were 2 healthy children (12-13 years old) with 20/40 or better corrected acuity. Optical coherence tomography confirmed the optic nerves, retina, and fovea were within normal variation. VEPs were recorded to checkerboard reversal and to onset/offset of horizontal gratings while simultaneously recording the electrooculogram (EOG). VEP epochs underwent Fourier analysis, and epochs were examined for phase consistency with the mean. Foveation periods were compared to video-oculography recordings from a separate session. Results: Optic nerve misrouting, such as crossed VEP asymmetry seen in albinism, or ipsilateral VEP asymmetry seen in achiasma, was not detected in either subject. By averaging only epochs in which EOG epochs showed foveation, VEP amplitude could be increased ≥59%. Averaging the VEP only on epochs with consistent phase at Oz increased VEP amplitude by ≥twofold; subsequent EOG epochs after this analysis mostly contained foveation periods or minimal EOG activity. Latency varied <14 ms across all analyses. Conclusions: The checkerboard reversal VEP signal is dependent on foveation periods in subjects with INS despite good visual acuity. Reduction in VEP amplitude due to retinal image motion induces noise and/or lack of phase locking in the VEP epochs. Selective averaging of epochs based on phase consistency improves the extraction of a VEP signal, likely when retinal image motion is minimized. [ABSTRACT FROM AUTHOR]