Heterophoria is the relative deviation of the eyes in absence of fusional vergence. Fusional vergence can be deprived by, for example, occluding one eye while the other fixates a visual target. Then, the occluded eye will presumably deviate from its initial position by an amount that corresponds to the heterophoria. Its assessment in clinical practice is crucial for the diagnosis of non-strabismic binocular dysfunctions such as convergence insufficiency. Traditional clinical methods, like the cover test or the modified Thorington test, suffer from practitioner's subjectivity, impossibility to observe the occluding eye or unusual viewing conditions. These limitations could be overcome by using eye tracking systems to measure objectively the heterophoria. The main purpose of this study was to compare the performance of an automated and objective method to measure near heterophoria using an eye-tracker with two conventional methods: the cover-uncover test and the modified Thorington test. The eye tracking method gave us the possibility to measure the heterophoria as the deviation of the occluded eye (mimicking the cover test) or as the deviations of the occluded and fixating eyes (adhering to the theoretical definition of heterophoria). The latter method provided smaller results than the former, although on average the differences might not be clinically relevant. The proposed objective method exhibited considerably better repeatability than the two conventional clinical methods. It showed better agreement with the modified Thorington test than with the cover-uncover test, and a similar level of agreement was obtained between the two clinical methods. To conclude, the use of eye-trackers to measure heterophoria provides objective and more repeatable measures. As eye-trackers become common tools in clinical settings, their use to measure heterophoria should be the new gold standard.