Every cancer registry should be able to quantify the level of completeness of registration. The current study describes a routine quality control procedure in the Estonian Cancer Registry (ECR) for assessing the completeness of registration. The registry's database was compared with the databases of the Tartu University Lung Clinic and the Maarjamõisa Hospital of the Tartu University Clinics, and active retrieval to obtain missing cancer cases diagnosed in 1998 was carried out. The overall completeness of case ascertainment based on this study was 90.8%. As a result of this procedure, 67 cases of malignant neoplasms (1.1% of the total number of incident cancer cases for 1998) and 11 cases of other reportable neoplasms were detected and recorded at the ECR. Cancers of the lung, thyroid gland and prostate were most frequently under-notified. For these sites, the number of cancer cases for 1998 for Estonia as a whole increased 2.6%, 11.8% and 2.2%, respectively. To conclude, the existence of electronic databases is a positive development, but cancer registrars still need to employ labour-intensive methods to validate diagnostic codes and to decide whether to include in the ECR cases found by active retrieval. Based on the findings of our study, which is the first one of its kind in Estonia, the completeness of cancer reporting varied by cancer site, and it appeared to be a substantial concern for several sites.