Objective To study the medication usage in patients with severe acute respiratory syndrome (SARS). Methods The information of the medications of 680 patients with SARS in Xiao Tang Shan Hospital was collected by HIS system and classified by using computer model on the basis of disease factor. The usage time and cases, and cost of these medications were calculated. The defined daily dose (DDD) and drug utilization index (DUI) were analyzed. Results A number of 359 drugs in 17 categories were applied to 680 patients with SARS. Most cases used antibacterial agents, the DDDs of immunomodulator and vitamins were the highest, the usage duration of vitamins and infusion fluids were the longest among 17 kinds of the drugs. The cost of methylpredni-solone injection was the highest. The mortality rate, kinds of drugs and frequency of drugs were higher in type C, type D and serious SARS patients than that of type A and common SARS patients. Conclusions Many kinds of medications have been prescribed to SARS patients. The dosages of these medication are very high, especially glucocorticoids, immuneomodulator and nutrient agents. The computer model on the basis of disease factor is probably valid, rapid and easy to standardize.