About 35 new childhood cancer cases are diagnosed in Estonia (population 1.3 million in 2011) every year. Despite continuous improvements in the healthcare system and available cancer treatment options, the survival rates for childhood cancers have appeared to remain lower than the European average. These observations and the accompanying decrease in incidence led us to hypothesize that some nonfatal cases might be missing from the Estonian Cancer Registry (ECR). The aim of this study was to evaluate the completeness of reporting of childhood cancer cases to the ECR and its impact on the estimates of cancer incidence and survival. All cases of benign and malignant tumours, diagnosed in 2000–2011 among children aged 0–17 years and eligible for registration in the ECR, were included in the study. Completeness of reporting was evaluated for cases aged 0–17 years, and incidence and survival were analysed for cases aged 0–14 for international comparisons. The total number of new cancer cases increased from 459 to 515. Overall completeness of case ascertainment was estimated to be 89.5%. After adding the missing cases, the overall incidence rate increased from 12.9 to 14.9/100 000 (from 3.4 to 4.7 for leukaemias). The 2010–2014 period estimate of the 5-year survival increased from 70 to 76% for all sites combined and from 71 to 82% for leukaemias. In conclusion, the under-reporting of nonfatal childhood cancer cases to the ECR had an important impact on incidence and survival rates, causing a considerable underestimation of both.