In-utero xenotransplantation of stem cells in abnormal fetuses effectively treats several genetic illnesses. The current research aimed to evaluate structural and morphological alterations in the liver of rabbit fetuses following xenotransplantation of human Wharton's jelly-derived mesenchymal stromal cells (hWJ-MSCs), using a stereological technique. All hWJ-MSCs were isolated from the human umbilical cord, and their authenticity was established by flowcytometry and differentiation. At gestational day 14, the rabbits were anesthetized, and hWJ-MSCs were injected into the uteri of 24 fetuses. Twenty-two fetuses were born successfully. Ten rabbit liver specimens were prepared from injected fetuses including; eight rabbits on day three following birth and two rabbits on the 21st post-natal day. The non-injected fetuses were considered positive controls. The livers of the control and hWJ-MSCs-treated rabbits were fixed, processed, stained, and examined through stereological approaches. In the hWJ-MSCs-treated group, the mean liver weight and volume increased by 42% and 78% compared to the control group. The total volume of the hepatocytes increased by 63%, and that of sinusoids by three folds in the treated rabbits. The total volume of the central veins increased by 70%. The total number corresponding to hepatocytes in the experimental group increased by 112% compared to the rabbits in the control. The total volume of the hepatocyte nuclei in the experimental group increased by 117% compared to the rabbits in the control. After xenotransplantation of human MSCs, host tissue microenvironments (here, the rabbit liver) were altered and these included quantitative factors corresponding to the liver tissue and hepatocyte morphometric indices.