The aim of this study is to compare histological patterns and to estimate the burden of thyroid cancers in the two Wilayahs (departments) of El-Taref and Guelma in northeast of Algeria (total population 0.9 million), locally reputed as having different rates of endemic thyroid diseases and cancer. A retrospective analysis of central pathology registers and clinical records of patients with thyroid diseases, covering the period 2008–2012, was conducted. A total of 145 cases of thyroid cancers with histological confirmation were registered in the two Wilayahs during the period, with a female to male ratio of 5.9 : 1. Estimates of crude incidence rates suggested that thyroid cancers were twice as frequent in the Wilayah of Guelma compared to El-Taref (p < 0.05) with a tendency to occur at a younger age in resident of the Wilayah of El-Taref. Diagnoses of thyroid adenoma were more frequent in the Wilayah of Guelma, whereas the prevalence of other thyroid lesions, including goitre, was similar in the two Wilayahs. This first descriptive study on geographic variations in thyroid cancer in Northern Africa suggests that significant differences may occur in relation with environmental and lifestyle exposures.