Goiter remains prevalent in iodine-deficient communities of developing countries, such as Nigeria. It may present with cardiovascular abnormalities, including impaired heart rate variability (HRV) and arrhythmias. Impaired HRV has not been fully studied among patients in Nigeria despite the endemicity of goiter. We, therefore, aim to evaluate HRV and arrhythmic patterns among goiter patients in southwest Nigeria. A cross-sectional study involving 40 hyperthyroid, 40 euthyroid, and 20 hypothyroid participants, as well as 20 age- and gender-matched control participants, who all had cardiovascular evaluation, thyroid function tests, and 24-h Holter electrocardiogram monitoring. The mean ages among the hyperthyroid, euthyroid, hypothyroid, and control populations were 41.53 ± 14.90, 40.67 ± 12.29, 43.78 ± 11.49, and 46.92 ± 13.85 years, respectively. Cardiac arrhythmia was more prominent in the hyperthyroid and hypothyroid groups (p<0.001). The most common abnormalities of rhythm in the hyperthyroid group were sinus tachycardia and atrial fibrillation, while sinus bradycardia was the most common rhythm abnormality in the hypothyroid group. HRV indices (SD of all normal–normal intervals [SDNN], SD of the averages of normal–normal intervals [SDANN], and root mean squares of differences between adjacent normal–normal intervals [RMS-SD]) were all impaired in the hypothyroid and hyperthyroid goiter groups but normal in both the control and the euthyroid population (p<0.01). The duration of goiter, left atrial, and left ventricular dimensions were the predictors of cardiac arrhythmias and impaired HRV. In summary, cardiac arrhythmias and HRV abnormalities are relatively common in hypothyroid and hyperthyroid goiter patients. Early diagnosis and treatment of thyroid abnormalities will help prevent cardiac dysfunctions associated with thyroid diseases.