A root cause detection method for semiconductor fabrication process based on analysis of a defect distribution pattern of a wafer (wafer map) was developed. We show two methods of root cause analysis. One method is the comparison analysis that determines a tool of the root cause by searching a tool monitoring wafers having similar wafer map to a product wafer. The other method is the commonality analysis that finds the tool commonly processing product wafers having similar wafer maps. To search similar wafer map automatically, a comparison algorithm of two sets of distributed points was developed. This algorithm measures a similarity of two wafer maps based on density images whose pixel value shows corresponding defect density. The two methods including the developed algorithm were evaluated using the data obtained from a real semiconductor fabrication process. The accuracy of the comparison analysis method was 91.7% for 12 cases in which the tool of the root cause were detected, while false rate was 0% for 22 cases in which there are no similar patterns in tool monitoring wafers. For 6 cases that the tool of root cause were detected by the commonality analysis, the algorithm classified wafers into similar patterns and non-similar patterns correctly. These results show that the proposed methods are applicable to the semiconductor fabrication process.