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Abstract The Derogatis symptom checklist (SCL-90-R) and its short version, the Brief Symptom Inventory (BSI), are widely used instruments, despite the fact that their factor structures were not clearly confirmed. The goals of this research were to compare four measurement models of these instruments including one-factor, nine-factor, a second-ordered factor model and a bifactor model, in addition to testing the gender difference in symptom factors in a community sample. SCL-90-R was assessed in a large community survey which included 2710 adults who represent the population of Hungary. Statistical analyses included a series of confirmatory factor analyses and multiple indicator multiple cause (MIMIC modeling). The responses to items were treated as ordinal scales. The analysis revealed that the bifactor model yielded the closest fit in both the full SCL-90-R and BSI; however the nine-factor model also had an acceptable level of fit. As for the gender differences, women scored higher on global severity, somatization, obsession-compulsion, interpersonal sensitivity, depression and anxiety factors. Men scored higher on hostility and psychoticism. The bifactor model of symptom checklist supports the concept of global symptom severity and specific symptom factors. Global symptom severity explains the large correlations between symptom factors.