Background: The purpose of this study is comparison of the results between regression and multi-level analysis to find out factors influencing outcome indicators (in-hospital death, length of stay, and medical charges) of stroke patients. Methods: By using patient sample data of Health Insurance Review qqqamp; Assessment Service, patients admitted with stroke were selected as survey target and 15,864 patients and 762 hospitals were surveyed. Results: For the results of existing regression analysis and multi-level analysis, models were assessed through model suitability index value and as a result, the value of results of multi-level analysis decreased compared to the results of regression, showing it is a better model. Conclusion: Factors influencing in-hospital death of stroke patients were analyzed and as a result, intra-class correlation (ICC) was 13.6%. In factors influencing length of stay, ICC was 11.4%, and medical charges, ICC was 17.7%. It was found that factors influencing the outcome indicators of stroke patients may vary in every hospital. This study could carry out more accurate analysis than existing research findings through analysis of reflecting structure at patient level and hospital level factors and analysis on random effect.