Molybdenum (Mo) is an essential microelement for the health of animals and human beings, and high dietary intake of Mo can lead to pathological conditions. However, the cytotoxic effects of high levels of Mo on the renal cells in ruminants have not been reported. Therefore, this in vivo study in goats was designed to investigate the impact of Mo on kidney-related apoptosis genes, and histopathological and ultrastructural changes in renal cells using real-time quantitative polymerase chain reaction (RT-qPCR), light microscopy, and transmission electron microscopy. A total of 48 goats were randomly distributed in equal number into four groups and assigned with one of three oral treatments of ammonium molybdate (15, 30, and 45 mg Mo kg(-1) BW), while control group received no Mo. Kidney tissues were taken from individual goat at days 0, 25, and 50 for determining expression of apoptosis genes including Bax, Bcl-2, Cyt c, caspase-3, and Smac. The results revealed that the expression of Bax, Smac, Cyt c, and caspase-3 was significantly (P < 0.05 or P < 0.01) upregulated in renal cells, whereas Bcl-2 was downregulated (P < 0.01). Histopathological lesions showed degeneration of renal tubule, glomerular atrophy, and dilation of Bowman's capsule. In addition, ultrastructural injury that predicted varying degrees of vacuolization, irregularity, fission of the nucleus, and swelling of mitochondria was observed in the cytoplasma of cells in groups treated with 30 and 45 mg Mo kg(-1). This concluded that high levels of molybdenum, which induces apoptosis of caprine renal cells, might be involved in the mitochondrial intrinsic pathway.