OBJECTIVES: Previous reports have suggested an association between hypothyroidism and macrovascular complications in type 2 diabetes (T2DM) but the association with microvascular complications is not well documented. This study aimed to determine whether there were significant differences in these complications in patients with T2DM with and without hypothyroidism. METHODS: This was a retrospective, cross-sectional, case-control study from a single centre specialising in diabetes in South Africa. T2DM was defined by American Diabetes Association criteria. The cases were all patients treated for hypothyroidism and the controls were clinically and biochemically confirmed euthyroid, who were under follow up between 1 January and 1 July 2016. Chronic kidney disease (CKD) was defined as an estimated glomerular filtration rate (eGFR) of < 60 ml/min, determined by the CKD-epidemiology collaboration equation (CKD-EPI) and/or albumin/creatinine ratio > 3 mg/mmol. Diabetic retinopathy (DR) was defined as the presence of aneurysms, bleeds, exudates and new vessel formation on the retina examined by an ophthalmologist. Diabetic peripheral neuropathy (DPN) was defined as the presence of symptoms, loss of 128-Hz sensation and abnormal 10-gm monofilament. Cardiovascular disease (CVD) was defined as the presence of major adverse cardiovascular events (MACE). RESULTS: There were 148 cases and 162 controls. Compared to the controls, the cases were older (65.6 vs 59.4 years, p < 0.00001), more likely to be female (67.6 vs 39.5%, p < 0.0001) and white (89.2 vs 79.6%, p = 0.02), have a lower HbA level (7.5 vs 8.2%, p = 0.0001), eGFR (64.4 vs 72.7 ml/min, p = 0.0006) and triglyceride level (2.18 vs 2.55 mmol/l, p = 0.04), have a higher high-density lipoprotein cholesterol level (1.13 vs 1.02 mmol/l, p = 0.001), a longer duration of diabetes (14.8 vs 11.6 years, p = 0.001) and using fewer antidiabetic agents (1.82 vs 2.19, p = 0.001). There was a higher prevalence of CKD (44 vs 57.8%, p = 0.03) and CVD (59.3 vs 45.3, p = 0.06), and a trend towards higher DR (66.7 vs 47.6, p = 0.09). There was no difference in body mass index, hypertension, low-density lipoprotein cholesterol level (all patients received statin therapy), DPN and amputations. After adjusting for confounding factors, there was no association between CKD and DR, and hypothyroidism, but the trend to association with CVD persisted (OR 1.97. p = 0.07). CONCLUSIONS: Hypothyroidism in T2DM was not associated with microvascular disease after adjusting for confounding factors. There was a nearly two-fold risk of CVD. The study is limited by the retrospective and observational design.