The aim of this study was to compare the formal thought disorder (FTD) in the acute episode of schizophrenia (SCHZ) and bipolar affective disorder (BPAD), and to determine the FTD dimensions associated with BPAD. The study included a total of 34 SCHZ patients not meeting the standardized remission criteria and 20 patients in BPAD manic episode. The patients completed the Positive and Negative Syndrome Scale (PANSS), the Clinical Global Impression Scale (CGI), the Young Mania Rating Scale (YMRS), the Hamilton Depression Rating Scale (HAM-D) and the Thought and Language Disorder Scale (TALD) in order to assess FTD. The association of FTD with the diagnoses was analyzed by a logistic regression model including the TALD factors and the SCHZ and BPAD groups. Statistically significant differences were not determined between the demographic features, the CGI scores and the TALD objective positive factor scores of the SCHZ and BPAD groups. The objective negative and subjective negative factors (p<0.001 for all) were higher in SCHZ group and the subjective positive factor were significantly higher in BPAD group (p=0.028). In the logistic regression model, the TALD subjective positive factor was associated with BPAD diagnosis, and the objective negative factor was associated with SCHZ diagnosis. In the BPAD group, the TALD total score correlated positively with the manic episode severity, and the scores on the subjective negative and subjective positive factors correlated negatively with disease duration. The study results show that FTD is common to the acute episodes of both SCHZ and BPAD and that assessment of the subjective positive FTD symptoms and objective negative FTD symptoms may be useful to differentiate the acute episode of SCHZ from the BPAD manic episode.