Abstract: Objective To analyze gender, area differences and age trends in congenital diseases among disabled children in Sichuan Province, so as to provide scientific basis for developing prevention and control strategies for these diseases.Methods A total of 21 059 diagnosed congenital diseases corresponding to 18 897 disabled children who applied for medical authentication between 2004 and 2015 in Sichuan Province were coded according to the Tenth Revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10). Gender, area differences and age trends in the coded congenital diseases were analyzed.Results Gender differences showed that the proportion of congenital heart disease in females was significantly higher than that in males (30.85% vs 19.08%), the proportions of congenital malformations of brain and congenital musculoskeletal deformities in males (7.24% and 4.76%) were significantly higher than those in females (5.94% and 3.92%). Age trends analysis showed that the proportions of congenital malformations of spine and bony thorax increased with age, the proportions of congenital heart disease, congenital malformations of brain, Down's syndrome decreased with age (all P<0.05). Area differences showed that Down's syndrome and congenital lens malformations were relatively higher in urban areas, while congenital musculoskeletal deformities, reduction defects of upper limb, cleft lip and palate were relatively higher in rural areas.Conclusions Gender, age differences and area trends exist among children with congenital anomalies in Sichuan Province. Effective prevention strategies should be developed to control congenital diseases and reduce the reproductive risk of families with congenital disabled children.