Objective To study anatomical and histological differences on hearts and lungs between α1,3-galactosyltransferase(GGTA1)gene-deficient cloned pigs and noncloned Bama miniature pig(as donor cell for somatic cell nuclear transfer). Methods Anatomical and histological structures on hearts and lungs of two α1,3-galactosyltransferase gene-deficient cloned pigs (BM164，BM155) and one healthy noncloned Bama miniature pig(BMM2) were observed by using gross anatomy and HE staining. Results The heart of noncloned Bama pig was inverted conical, anterior border convexity and posterior border short and straight, obvious coronary sulcus, sulcus longitudinalis sinister and sulcus longitudinalis dexter. The cardiac wall was divided into three layers. The endocardium was thin and there were some Purkinje fibers in the ventricle. The cardiac muscle fibers arranged densely, clear cross striation and fewer intercalated disk in the cardiac muscle. The epicardium was thick, and had obvious unmyelinated nerve fibers. Compared with noncloned Bama pig, the hearts of GGTA1 gene-deficient cloned pigs showed no significant anatomical and histological differences. The lung of noncloned Bama miniature pig was pink spongy, soft and light. Histological observation showed that there were some cartilages around small bronchi, some tracheal glands and inflammatory cells in submucosa, few dust cells and thicker alveolar wall. Bronchial mucosal folds were finger-like projections into the lumen, which was infiltrated by some inflammatory cells. The structures of anatomical and histological structures in lungs between α1,3-galactosyltransferase gene-deficient cloned pigs and noncloned Bama pig were basically same. Conclusion The hearts and lungs of GGTA1 gene-deficient cloned pigs and noncloned Bama miniature pig showed no significant anatomical and histological differences.