Background Worldwide immunization coverage shows an increase in the past years but the validity of the official reports for measuring change over time has been questioned. Facing this problem, donor supported initiatives like the Global Alliance for Vaccine and Immunizations, have been putting a lot of effort into assessing the quality of data used, since accurate immunization information is essential for the Expanded Program on Immunization managers to track and improve program performance. The present article, discusses the practices on record keeping, reporting and the support mechanism to ensure data quality in Mozambique. Methods A process evaluation study was carried out in Mozambique in one district (Cuamba) in Niassa Province, between January and March 2003. The study was based on semi-structured interviews, participant observation and review of the data collection materials. Results Differences were found for all vaccine types when comparing facility reports with the tally sheets. The same applies when comparing facility reports with district reports. The study also showed that a routine practice during supervision visits was data quality assessment for the outpatient services but none related to data consistency between the tally sheets and the facility report. For the Expanded Program on Immunization, supervisors concentrated more on the consistency checks between data in the facility reports and the number of vaccines received during the same period. Meetings were based on criticism, for example, why health workers did not reach the target. Nothing in terms of data quality was addressed nor validation rules. Conclusion In this paper we have argued that the quality of data, and consequently of the information system, must be seen in a broader perspective not focusing only on technicalities (data collection tools and the reporting system) but also on support mechanisms. Implications of a poor data quality system will be reflected in the efficiency of health services facing increased demands, with stagnant or decreasing resources.