Runs test is a mathematical tool to test the stationarity of electromyographic (EMG) signals. The purpose of this study is to investigate the effects of segmentation size on the stationarity of EMG signals in runs test. Six subjects participated in this experiment and performed isometric trunk exertions for twenty seconds at the load level of 25% and 50% MVC. The signals extracted from the erector spinae muscles were divided into the intervals of 1000ms and the stationarity of the signal in each interval was tested by the runs test. In this test, seven segmentation sizes such as 1.0, 2.0, 3.9, 7.8, 15.6, 31.3 and 62.5ms were applied. Additionally, two stationarity tests of reverse arrangements test and modified reverse arrangements test were used to verify the results of the runs test. In results, the segmentation size of 62.5ms showed the similar results with the other stationarity tests. However, the stationarity values among there tests were different each other when segmentation sizes other than 62.5ms were used. These results indicated the effect of segmentation size in runs test that needs to be considered to have consistent and sensitive result in stationarity test.