Endomyocardial fibrosis (EMF) is a cardiomyopathy with high prevalence in Sub-Saharan Africa with unclear etiology, pathogenesis and natural history. Most pathological abnormalities can potentially be diagnosed by echocardiography allowing surgery in some cases. With increasing availability of echocardiography in endemic areas for EMF we designed a study aiming at assessing its accuracy in defining EMF structural abnormalities pre-operatively, and describe pathological findings through detailed intraoperative examination and evaluation of histopathological changes in tissue obtained from excisional biopsies. Transthoracic echocardiography was performed pre-operatively to 29 patients with chronic severe EMF. All patients were submitted to excisional endomyocardial biopsies during surgery and careful standardized intra-operative evaluation was also done. Surgical and histopathological findings were compared to those obtained by echocardiography. Of the 29 patients studied, 16 had moderate lesions while 13 had severe disease. Their mean age was 12 (±4.6) years and 17 were males. All but one patient were in NYHA functional class III or IV at time of surgery. All patients had severe atrioventricular valve regurgitation with valves considered suitable for repair. We evaluated tissue from 25 left ventricles and 12 right ventricles. Endocardial thickening was the most prominent abnormality due to deposition of hyaline and cellular collagen underneath a layer of apparently normal endocardial endothelial cells. The mean endocardial thickness was 2,541 ± 1,707 μm. There was high agreement between echocardiographic and intraoperative findings, with the findings coinciding completely in 24 patients. Severe EMF assessed by echocardiography was associated with intense endocardial fibrosis on histology. In contrast, the presence of inflammation in peripheral blood was not associated with tissue inflammation. Structural abnormalities of chronic severe EMF are accurately diagnosed by transthoracic echocardiography, allowing this non-invasive technique to be used as the gold standard for diagnosis and surgical management of chronic EMF in endemic areas.