Anencephaly is the commonest congenital anomaly of nervous system where the rostral end of neural tube is malformed. In the present study, the thymus gland from an anencephalic fetus is compared with that of a normal stillborn term fetus. Thymus glands were fixed in neutral buffered formalin and processed for routine histological study. In addition to routine histological features, the study included characteristic features of the reticular epithelial cells, dendritic cells, immature T cells and the process of apoptosis of the thymocytes, using an array of markers including cytokeratin, S100, terminal nucleotidyl transferase and CD99. Cytokeratin in the anencephalic fetus was diffusely distributed all over the lobule, compared to normal thymus which showed positivity in medulla & reticular epithelial cells of Hassall’s corpuscles. Nature and distribution of dendritic cells of anencephalic thymus did not reveal noticeable difference from the thymus of the normal still born fetus. Immature T cells in anencephalic fetus were well pronounced around Hassall’s corpuscles in medulla. Degree of apoptosis of thymocytes was far less compared to the thymus in normal fetus. Decreased degree of apoptosis might have led to thymic hyperplasia as reflected by reduced expression of CD99 in the anencephalic fetus.