Purpose. To evaluate the results in the use of different modes for alternating presentation of stimuli in the orthoptic treatment of strabismus in children. Material and methods. The study included 41 patients with a nonparalytic strabismus (30 children with esotropy and 11 children with exotropy) aged from 7 to 16 years. For additional studies of binocular functions, we used a modified Bagolini test and our own stereo-test created for the conditions of anaglyph separation of visual fields. During the first examination the results with all the used stereo-tests (the Flytest, the Lang-test, and the stereo image that we created) were negative. Besides to the static presentation of test images, three different modes of alternating presentation of stimuli were used: 1) with consecutive monocular presentation of visual stimuli corresponding to the right and left eye; 2) with the presence of an empty interval between monocular phases; 3) with the presence of a binocular phase between monocular phases. The duration of the monocular and binocular phases, as well as the empty interval, was regulated by the researcher. Depending on the results of the examination, an optimal mode of alternative presentation of stimuli for the orthoptic tr eatment was selected individually. Results. In the duration of the monocular phase 50 ms in combination with the duration of an empty interval 50 ms, the majority of children (32 of 41) with strabismus were able to have stereovision. As a result of orthoptic exercises, the number of patients capable of bifoveal fusion increased from 24.4% to 48.8%. Stereovision appeared in 39% of children according to the Fly-test and in some cases according to the Lang-test. In all children with moderate amblyopia the visual acuity increased on average from 0.23±0.01 to 0.52±0.05 (p<0.001), in children with mild amblyopia the visual acuity increased on average from 0.66±0.02 to 0.93±0.01 (p<0.001). A reduction of the strabismus angle or an elimination of postsurgical microdeviation occur in one-third of children. Conclusion. The proposed method for the study of binocular functions in patients with strabismus allows to evaluate the ability to the bifoveal fusion and stereo perception not only with static presentation of visual stimuli, but also with the use of different modes of their alternating presentation. The most favorable mode for the elimination of functional inhibition is the mode of alternating presentation of stimuli with the presence of an empty interval not less than 50 ms between the monocular phases, which are also not less than 50 ms. This mode with the combination of monocular phase duration and empty interval duration in the range from 30 to 60 ms creates the most favorable conditions for the appearance of the stereo effect in the majority of the patients. The use of optimal individually chosen regime of alternating presentation of the stimuli allows to improve significantly the binocular functions, to increase the visual acuity, and in some cases to reduce the angle of strabismus or to eliminate postsurgical microdeviations.