Background A crucial goal of infectious disease surveillance is the early detection of epidemics, which is essential for disease control. In China, the current surveillance system is based on confirmed case reports and only covers notifiable diseases. In rural China, it is not practical for health units to perform laboratory tests to confirm disease and people are more likely to get 'old' and emerging infectious diseases due to poor living conditions and closer contacts with wild animals and poultry. Syndromic surveillance which collects non-specific syndromes before diagnosis has great advantages in promoting the early detection of epidemics and reducing the necessities of disease confirmation. It will be especially effective for surveillance in resource poor settings. Objectives The objective is to improve the early detection of epidemics in rural China by integrating syndromic surveillance with case report surveillance system. This involves three main phases: (1) the development of an integrated surveillance system; (2) the implementation of this system; (3) the evaluation of this system. This project will contribute to knowledge, experience and evidence with regard to the development and implementation of an integrated surveillance system for the early warning of epidemics in similar settings. Methods This is an intervention study. The intervention tool will be an integrated surveillance system, combining syndromic surveillance with the existing case report surveillance in four selected counties in China. In order to evaluate the early warning capability of the new added syndromic surveillance, the timelines and validity of the alert signals triggered from syndromic surveillance will be compared against those from corresponding case report surveillance (as a reference) for the same region and time period. The acceptability, feasibility and economic evaluation of the whole integrated surveillance system will be conducted in a before and after study design.