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Background Congenital heart disease (CHD) is a common heart condition which does considerable harm to the health of children and adolescents. CHD epidemiological characteristics of Tibetan children whose ages ranged from 4 to 18 years were investigated in Qinghai Province. Methods A total of 32 578 Tibetan children, living at altitudes of 2535 m, 3600 m and 4200 m, were examined using a three-stage protocol: prescreening, rechecking and diagnosis using a color Doppler. The distribution of CHD at different altitudes was analyzed together with differences in occurrence according to age and gender. Results A total of 235 CHD cases were discovered. The total prevalence of CHD was 7.21%o. Prevalence of CHD has been shown to increase along with increase in altitude with 5.45%0 at an altitude of 2535 m, 6.80%0 at 3600 m and 9.79%. At 4200 m. There were no statistically significant differences between the prevalence at 2535 m and 3600 m 0(2=1.594, P ＞0.05). However, there was a significant difference between the prevalence at 2535 m and 4200 m (X2=7.002, P＜0.01). Also, apparent differences existed between the prevalence at 3600 m and at 4200 m (X2=5.540, P＜0.05). There was no statistically significant difference in prevalence according to age at an altitude of 2535 m, but the rate of CHD increased significantly along with increasing age at 3600 m and 4200 m. The total prevalence ratio of children aged from 16 to 18 years was significantly higher than that of children from 4 to 7, and from 8 to 12 with X2 values of 10.79 (P＜0.005), and 5.60 (P＜0.05) respectively. Within the constituent ratio of CHD, the prevalence of atrial septal defect (ASD) was the highest at 39.10%, followed by the prevalence of ventricular septal defect (VSD) at 32.8% and patent ductus arteriosus (PDA) at 24.7%. Furthermore the proportion of the four categories of CHD varied at different altitude levels: at 2535 m, of those diagnosed with CHD, the prevalence rate of VSD was the highest at 43.5%, at 3600 m ASD was the highest at 42.8% and at 4200 m, PDA was the highest at 50.8%. Conclusion The epidemiological characteristics of CHD in Tibetan children may be associated with altitude levels.