Abstract: Objective To evaluate the quality index system for internet based notifiable infectious disease reporting in China since 2004. Methods The monthly and annual evaluation data from 2004 to 2013 was collected, then card information in the reporting system, field investigation of report quality and organization codes in standard coding management system were combined for comprehensive analysis and discussion. Results The average monthly miss report rate in counties showed a downward trend during 2006-2010, and only two counties had no report in 2010. The overall reporting rate of major infectious diseases was in increase and reached the highest: 95.39% in 2012. The rate of normal operation of the network was 99.10% in 2013, but to the limited maintenance facilities, this indicator could not reflect the coverage of network reporting system on national medical institutions. The timeliness of medical diagnosis reporting increased year by year during 2006-2013 and the average monthly timely reporting rate was 99.75% in 2013. The consistent rate between the diagnosis time and reporting time was low. The timely verifying rate of the report increased year by year during 2006-2013, the average monthly verifying rate was 99.89% in 2013. But problems still existed in some verified reporting cards, such as information miss, logic errors, mis-filling of age or occupation, diagnostic classification in consistent with diagnostic criteria and standards, etc. Monthly repeated reporting cards decreased year by year during 2006-2013 and the proportion of repeated reporting cards decreased to 0.0012% in 2013. The repeated cards which system recognized automatically declined due to the errors in the cards. Conclusion The quality evaluation index system well covered the area of data collection and management, and statistical methods of evaluation index were also constantly improved. The relevant field research was still needed to evaluate the quality of reporting data in the system.