This study aimed to evaluate the prevalence of heterotropia and heterophoria in Iran. This was a cross-section study undertaken in 2013 with the target population of grade 1 (seven-year-old) children. Seven cities across different geographical locations were included with multistage randomised cluster sampling and equal numbers of boy and girl schools. Assessment was with non-cycloplegic automated refraction, visual acuity with E Snellen chart at six metres, cover test at near and distance fixation, cycloplegic refraction plus lensometry. Of the 3675 children recruited (47.8% female), 92 children were found to have strabismus – a prevalence of 1.68%. The prevalence was calculated as 2.17% for boys and 1.27% for girls. Exotropia was the most common strabismus (1.27%). Esotropia occurred in 0.44%, hypertropia in 0.1%, heterophoria in 32.98%, constant strabismus in 0.73% and intermittent strabismus in 0.96%. Amblyopia was present in 23.77% in strabismic and 1.43% in non-strabismic children. There were greater odds in amblyopia in esotropia than exotropia. The results support attention to screening and treatment of amblyopia in strabismus.