Introduction: Adiponectin can influence glucose and lipid metabolism and body weight. As thyroid hormones play an important role in general metabolism and body weight regulation, changes in serum levels of adiponectin in thyroid dysfunctions are likely. The current study aimed at evaluating the association between serum adiponectin level and thyroid dysfunction in subclinical hypothyroid and hyperthyroid individuals. Materials and Methods: This study was performed on 68 subclinical hypothyroid and hyperthyroid subjects (in equal groups) and 34 euthyroid who referred to the Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences. In all participants, serum levels of adiponectin, TSH, FT3, FT4, insulin, glucose, lipid profiles and BMI were assessed. Serum adiponectin, FT3, FT4 and TSH were measured by ELISA, Electrochemiluminescence and Immunoradiometric assay (IRMA), respect­tively. Data were analyzed by T-test, One-Way ANOVA and Pearson correlation using SPSS 16. Results: Serum concentrations of adiponectin in both the hypothyroid and hyperthyroid groups (11.91±5.02 and 11.87±5.84 ng/ml, respectively) were remarkably lower than the control group (15.13±5.88 ng/ml), (P<0.05). There was no significant correlation between serum levels of adiponectin and TSH, FreeT3, FreeT4, or BMI. Conclusion: Decrease in serum levels of adiponectin in hypo^- and hyperthyroid individuals may indicate a significant association between adiponectin concentrations and thyroid dysfunction.