OBJECTIVES: (1) To explore differences in educational attainment between children born with isolated clefts and the general population at ages 5, 7 and 11 years; (2) to describe longitudinal changes in attainment among children with cleft through primary education. DESIGN: Analysis of Cleft Registry and Audit Network data linked to national educational outcomes. SETTING: English state schools. PATIENTS: 832 children born with isolated cleft, aged 5 years in 2006-2008. MAIN OUTCOME MEASURES: Difference in teacher-assessed attainment between children with a cleft and general population at each age, for all children and by cleft type. Percentage of children with low attainment at age 5 years who had low attainment at age 11 years, for all children and by cleft type. RESULTS: Children with a cleft had lower attainment than the general population in all subject areas (Z-score range: -0.29 (95% CI -0.36 to -0.22) to -0.22 (95% CI -0.29 to -0.14)). This difference remained consistent in size at all ages, and was larger among children with a cleft affecting the palate (cleft palate/cleft lip and palate (CP/CLP)) than those with a cleft lip (CL). Of 216 children with low attainment in any subject at age 5 years, 54.2% had low attainment in at least one subject at age 11 years. Compared with children with CL, those with CP/CLP were more likely to have persistent low attainment. CONCLUSIONS: An educational attainment gap for children born with isolated clefts is evident throughout primary education. Almost half of children with low attainment at age 5 years achieve normal attainment at age 11 years.