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To assess fixation stability in patients, a scanning laser ophthalmoscope (SLO) has typically been required. Disadvantages of this technique include the need for a fixed viewing distance and rigid head support. Some modern infrared eyetrackers do not have these constraints. The purpose of this study was to compare fixation stability measurements made with these instruments.Normal subjects were asked to fixate a 2.5° high cross while fixation was measured with a SLO and an infrared eyetracker. Bivariate contour ellipse areas were calculated.There was a linear relationship between the bivariate contour ellipse areas measured using each instrument. Bivariate contour ellipse areas returned from the eyetracker were larger. There was no difference in test-retest variability between the instruments.The eyetracker indicates fixation to be less stable than the SLO does, perhaps because of eye movements to compensate for small head movements. Our eyetracker can be used to analyze fixation when viewing images at any distance, without the need for head immobilization. The eyetracker and the SLO complement each other in the investigation of visual behavior.