The aim of the study is to review the criteria for data quality assessment, and, on the basis of them, to evaluate monitoring systems of influence and other acute upper respiratory tract infection (AURTI), functioning in the city of Vilnius. The EC legislation provides for the following data quality criteria: relevance, accuracy, timelines, punctuality, accessibility, clarity, comparability, and coherence. The implementation of these criteria is closely related with the regulation and organisation of data collection. The later create necessary conditions to ensure quality of information collected by influenza and AURTI system. There are currently two monitoring systems in Lithuania - based on sample surveys and health statistical reports “Sveikata”. The study showed that the incidence of influenza and AURTI registered by two systems had statistically significant differences. An increase in the incidence, registered in the statistical reports, by 1 was followed by 1.6 higher increases by sample surveys. When evaluating the incidence rate in the 7 health care institutions, big data scatter and differences were found among two systems. Therefore different monitoring systems in the regions produce statistically significant different results. It is likely that due to personal responsibility of the physician, the quality of the sample survey system is higher; this attitude, however, needs further research.