There is growing evidence for deficits in motion perception in amblyopia, but these are rarely assessed clinically. In this prospective study we examined the effect of occlusion therapy on motion-defined form perception and multiple-object tracking. Participants included children (3-10years old) with unilateral anisometropic and/or strabismic amblyopia who were currently undergoing occlusion therapy and age-matched control children with normal vision. At the start of the study, deficits in motion-defined form perception were present in at least one eye in 69% of the children with amblyopia. These deficits were still present at the end of the study in 55% of the amblyopia group. For multiple-object tracking, deficits were present initially in 64% and finally in 55% of the children with amblyopia, even after completion of occlusion therapy. Many of these deficits persisted in spite of an improvement in amblyopic eye visual acuity in response to occlusion therapy. The prevalence of motion perception deficits in amblyopia as well as their resistance to occlusion therapy, support the need for new approaches to amblyopia treatment.