Objective To study the alteration of peripheral lymphocyte subsets in severe acute respiratory syndrome (SARS) patients and to help improve the early diagnosis of the disease. Methods Anti-coagulating blood samples from 98 SARS patients in the acute phase, 56 normal healthy blood donors, and from patients infected by HIV, CMV and EBV were collected. The T lymphocyte subsets were counted by flow cytometry using fluorescence-labeled specific monoclonal antibodies. Results A significant decrease was observed in all SARS patients in their peripheral CD4+ and CD8+ T lymphocyte absolute counts [256(104)×106/L and 256 (117)×106/L, respectively], which were also lower than those of the patients infected with HIV, CMV and EBV. All patients infected with HIV, CMV and EBV had significantly higher CD8+ T lymphocyte counts in comparison with normal controls. Conclusions Decrease of both CD4+ and CD8+ T lymphocytes of patients is related to onset of SARS. T lymphocyte subset analysis would help improve the early diagnosis of the disease.