Objective: The metabolic syndrome (MS) is highly prevalent among patients with bipolar disorder (BD), and may affect progression, functioning, and comorbid conditions in BD. The aim of this study was to investigate the effect of clinical variables and MS on overall functioning and specific areas of functioning in patients with BD. Methods: A total of 210 participants (140 participants with BD I and BD II in remission and 70 non-psychiatric control subjects) were included. The investigators administered the Young Mania Rating Scale (YMRS), the Bipolar Depression Rating Scale (BDRS), the Global Assessment of Functioning Scale (GAF), and the Bipolar Disorder Functioning Scale (BDFS). The participants completed the Beck Depression Scale (BDS) and the Beck Anxiety Scale (BAS). MS was diagnosed according to the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criteria. Hierarchical regression analysis was used to investigate potential correlations of comorbid MS with clinical variables and level of functioning. Results: Level of functioning did not differ between patients with and without MS. However, there were significant correlations between the level of functioning subscales and the number of depressive episodes (p = 0.033), level of general functioning (p = 0.012), duration of illness (p = 0.012), BDS (p = 0.005), BDRS (p = 0.021), BAS total scores (p = 0.021), number of hypomanic episodes (p = 0.022), number of hospitalizations (p = 0.003), employment status (p = 0.032), and diagnosis of BD I (p = 0.007) and BD II (p = 0.044). Conclusion: Our findings suggest that clinical variables had a greater effect on functioning than MS in BD patients.