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Objective: This study was to define the clinical effect on the clinical decision support system (CDSS) for prescribing antibiotics integrated with the order communication system in a National Hospital. Method: We extracted data collected before integrating the CDSS of 4,406 adult patients in 2007 and data collected after integrating the CDSS of 4,278 adult patients in 2009. These patients were 50.4% and 45.2% of all patients admitted in 2007 and 2009, respectively. The clinical effect was defined as the proportion of prescribed antibiotics, the length of antibiotics use, and the DDDs (defined daily doses) of antibiotics per 1,000 patient-days using these retrospective data. Results: There were a significant change in the proportion of patient prescribed penicillins with extended spectrum (OR=0.55, p=001), penicillins included beta-lactamase inhibitors (OR=0.75, p<.001), 3rd cephalosporin (OR=1.47, p<.001). The mean of the length of antibiotics use was decreased statistically from 6.09±5.48 to 5.85±5.51 days (p=.003). The DDD of glycopeptides was decreased from 24.43 DDD to 19.55 DDD per 1000 patient-days. The DDD of 3rd cephalosporins was also decreased from 15.88 to 11.65. Conclusion: Therefore, the clinical decision support system for prescribing antibiotics was effective for the clinical outcomes.