Objectives. Microstate studies of electroencephalograms (EEGs) on schizophrenia (SCZ) and bipolar disorder (BD) demonstrated categorical differences. The relationship between microstate indices and clinical symptoms in each group, however, remained unclear. Our objective was to examine associations between EEG microstates and the core features of SCZ and BD. Methods. This study examined the resting EEG data of 40 patients with SCZ, 19 patients with BD (12 BD type I and 7 BD type II), and 16 healthy controls. EEG topographic maps were divided into four canonical microstate classes: A, B, C, and D. The Positive and Negative Syndrome Scale (PANSS), Young Mania Rating Scale, Hamilton Depression Rating Scale (HAMD), and Global Assessment of Functioning (GAF) were used to measure clinical symptoms and global functioning. Results. There was a significant inverse correlation between the proportion of time spent in microstate class A and GAF in patients with SCZ but not BD. Furthermore, the occurrence of microstate class A was positively correlated with the Positive Scale scores of the PANSS. Nevertheless, there were no group differences between the microstate classes. Conclusions. The results of this study indicate a negative correlation between microstate class A and global functioning in SCZ but not in BD. The association may be mediated by positive symptoms of SZ. Neural mechanisms underlying this relationship require further investigation.