The aim of this study was to carry out quantitative analyses of eye movements during the cover test on a group (n = 57) of asymptomatic emmetropes. Eye movements were recorded during an automated cover test while subjects fixated a distance (3.4 m) and near (0.4 m) target. There was a significant difference between the amplitude of phoria measured after 2 s of occlusion compared to 10 s (P < 0.01). The mean phoria after 10 s of occlusion was 0.1° (eso) for distance fixation and 1.6° (exo) for near fixation. The distribution was approximately normal for both distance and near fixation but the standard deviation was greater for near (2.0°) than distance fixation (1.4°). The pattern of eye movements during the recovery phase was more complex than is often assumed, in many cases consisting of a variety of saccadic and vergence movements involving both the covered and ‘fixing’ eye. The latency of the first recovery movement was significantly shorter for exophoric than esophoric deviations (P < 0.01) and the latency of some recovery movements were very short (< 150 ms).