Abstract : Immunization information systems (IISs), otherwise known as registries, are confidential, population-based databases that record all immunization related activities. This study aimed to evaluate immunization information system data quality between paper-based system and electronic based system comparatively. It is a cross-sectional study design for evaluation of data quality of reports generated by both paper-based immunization information system and electronic-based immunization information system, using WHO Data Quality Self-assessment Tool. Descriptive statistics (means) were used to describe the data acquired from the evaluation. An independent t-test was used to compare data quality between paper-based immunization information system and electronic-based immunization information system. As a result, it was found that when comparing its data quality, there is a significant difference in mean score for data quality generated between paper-based immunization information system and electronic-based immunization information system with p value of <0.001.Conclusively, this study has shown that even though paper-based immunization information system is generally good in term of its data quality, but electronic-based immunization information system proved to have better data quality.