Purpose To evaluate sensorimotor outcomes among children in the Infant Aphakia Treatment Study (IATS). Methods Secondary outcome analysis was performed in this randomized, multicenter, clinical trial comparing treatment of unilateral aphakia with a primary intraocular lens (IOL) or contact lens (CL) correction. The alignment characteristics and sensory status of children through age 5 years were evaluated. Results In the IATS study, 91 of 112 children (81%) developed strabismus through age 5 years. Of 34 infants who were orthotropic at near 12 months after cataract surgery, at age 5 years 14 (41%) were orthotropic at distance, and 15 (44%) were orthotropic at near at age 5 years without strabismus surgery. Eight of 56 children (14%) in the CL group and 13 of 56 (23%) in the IOL group were orthotropic at distance (P = 0.33) at 5 years of age and had no history of strabismus surgery. Thirteen of 48 (27%) who underwent cataract surgery prior to 49 days of age compared to 8 of 64 (13%) who had surgery after 49 days were orthotropic (P = 0.085). Median visual acuity in the operative eye was 0.4 logMAR (20/50) for children with orthotropia or microtropia (<10Δ) versus 1.10 logMAR (20/252) for strabismus ≥10Δ (P = 0.0001). Stereopsis was detected in 12 of 21 children (57%) with orthotropia versus 16 of 89 (18%) children with strabismus (P = 0.0006). Conclusions IOL placement does not reduce the development of strabismus after monocular congenital cataract surgery. Improved ocular alignment by age 5 years correlated strongly with improved visual acuity and stereopsis.