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Background  Scrub typhus is a life-threatening disease caused by  Orientia tsutsugamushi , and specific antimicrobial medicine is available .  Early and accurate diagnosis is essential for reducing the risk of severe complications and death. In this study, we aimed to evaluate the case diagnosis situation among medical care institutions and geographical regions in China, and the results will benefit both clinical practice and the disease surveillance system.    Methods  We extracted individual scrub typhus case data 2006–2016 from a national disease surveillance system in China. The diagnosis category and interval time from illness onset to diagnosis were compared among three levels of medical care institutions and provinces. The descriptive analysis method was performed in our study.    Results  During the 11-year study period, 93 481 scrub typhus cases, including 57 deaths, were recorded in the nationwide surveillance system. The overall proportion of laboratory-confirmed cases was only 4.7%, and this proportion varied greatly among primary medical centres (2.8%), county level hospitals (4.2%), and city level hospitals (6.3%). Notably, the proportion of laboratory-confirmed cases has consistently decreased from 16.3% in 2006 to 2.6% in 2016, and the same decreasing trend was found among all three levels of medical care institutions. The interval from illness onset to case diagnosis (T diag ) for all cases was 5 days (interquartile range [IQR]: 2–9 days) and decreased from 7 days (IQR: 3–11 days) in 2006 to 5 days (IQR: 2–8 days) in 2016. The risk of death for patients with a T diag  of > 7 days was 2.2 times higher ( OR  = 2.21, 95%  CI : 1.05–5.21) than that of patients with a T diag  of < 2 days.    Conclusions  The interval time from illness onset to diagnosis for scrub typhus cases decreased greatly in China; however, the diagnosis rate of cases with laboratory-confirmed results must be increased among all levels of medical care institutions to reduce both the risk of death and the misuse of antibiotics associated with scrub typhus.    Electronic supplementary material  The online version of this article (10.1186/s40249-019-0566-0) contains supplementary material, which is available to authorized users.

Evaluation of scrub typhus diagnosis in China: analysis of nationwide surveillance data from 2006 to 2016