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Abstract Background Hypothyroidism (sub-clinical and overt) and metabolic syndrome are recognized risk factors for atherosclerotic cardiovascular disease. This study is an effort to identify the proposed association between these two disease entities and the risk factors involved in this association. Methods A cross – sectional study from a tertiary care teaching hospital in Chennai city, South India. 420 patients with metabolic syndrome (NCEP – ATP III criteria) were included in the study group. 406 appropriately age and sex matched controls having no features of metabolic syndrome (0 out of the 5 criteria) were compared with the study group. The study extended over a 5 year period. TSH, FT4 were measured for both the groups using electrochemiluminescence immuno assay. HsCRP was measured for all the patients in the study group. The baseline characteristics between the groups were compared with Student's't' test. Chi-square test was used to analyze the association between metabolic syndrome and hypothyroidism (overt and sub-clinical). Logistic regression analysis was applied to identify the association between hypothyroidism and the patient characteristics in the study group. Results Of the 420 patients in the study group, 240 were females (57.1%), 180 were males (42.9%) with mean age 51 ± 9.4 years. Of the 406 patients in the control group, 216 were females (53.2%), 190 males (46.8%) with mean age 49 ± 11.2 years. In the study group, 92 had sub-clinical hypothyroidism (SCH) (21.9%), 31 were overtly hypothyroid (7.4%) and 297 were euthyroid (70.7%). In the control group 27 patients had sub-clinical hypothyroidism (6.6%), 9 patients had overt hypothyroidism (2.2%) and 370 patients were euthyroid (91.2%). On comparison SCH (P < 0.001) and overt hypothyroidism (P < 0.001) were significantly associated with the study group as compared to the control group. Logistic regression analysis recognized the association between female gender (P = 0.021) and HsCRP (P = 0.014) with sub-clinical hypothyroidism and female gender (P = 0.01) with overt hypothyroidism in the study group. Conclusion Hypothyroidism is associated with metabolic syndrome and females are more at risk. Metabolic syndrome patients with a raised HsCRP are at significant risk of having sub-clinical hypothyroidism.