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Introduction: This paper assesses both patients' perspectives on the differences in primary care quality between traditional Tibetan medicine (TTM) hospitals and western medicine (WM) hospitals and the efficacy of the government's investment in these two Prefecture-level primary care structures in Tibet. Method: A validated Tibetan version of the Primary Care Assessment Tool (PCAT-T) was used to collect data on 692 patients aged over 18 years old, who reported the sampling site was their regular source of health care. T-tests were performed to compare the separate and total primary care attributes between WM hospitals and TTM hospitals. Multiple linear regression analysis was conducted to examine the association of the health care setting with primary care attributes while controlling for socio-demographic, health service use and health status characteristics. Results: Compared to WM hospitals, the results showed that TTM hospitals had patients who were older (15.8 % versus 8.4 % over 60 years); with lower education levels (66.0 % versus 35.8 % with below junior high school ) and income levels (46.9 % versus 26.5 % with annual household income below 30,000RMB); more likely to be married (79.2 % versus 60.5 %); made less frequent health care visits; and had higher self-rated health status. Overall, patients assessed the primary care performance in TTM hospitals significantly higher (80.0) than WM hospitals (74.63). There were no differences in health care assessment by patient gender, age, income, education, marital status and occupation. Conclusions: TTM patients reported better primary care experiences than patients using WM hospitals, which validated the government's investment in traditional Tibetan medicine. [ABSTRACT FROM AUTHOR]