Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. Concentrations of heavy metals (As, Fe, Mn, Cu, Pb, Cd, Cr, Zn, and Hg) were examined in the tissues of Chinese alligators to elucidate the background distribution of these metals in the alligator body. Generally, within the body compartments, metal concentrations were high in liver, kidney, and heart, and low in pancreas and gonad. Study of heavy metal levels in the feces and eggs of Chinese alligator suggested that Chinese alligators could reduce body burden of toxic substances by excreting them to feces and/or sequestrating them into eggs to a lesser extent. In addition, to test whether eggshell or egg membrane could be used as surrogates to measure heavy metal load in egg contents, the correlation of metal concentrations between three egg compartments was determined. Of the nine elements analyzed, concentrations of iron, copper, and zinc in the shell membrane were highly correlated with the levels in egg contents, whereas no metal was significantly correlated between eggshell and egg contents. This suggested that the shell membrane could be a useful bioindicator for Fe, Cu, and Zn contaminations in the eggs of Chinese alligator. In a comparison of metal contents in the eggs of individuals from the Anhui captive population, the wild population in Anhui Province, and those of the Changxing captive population, higher Cu, Zn, and Cd levels and a lower Pb level were found in the Changxing individuals, indicative of specific pollutants in different areas. In addition, the majority of metal elements in the muscles of Chinese alligators and American alligators are in the same ranges. As a result of the data found in the eggs of the two alligator species, the Chinese alligators may be exposed to a higher level of metal pollutants. The study provided measurement of the heavy metal distribution in the endangered Chinese alligator for the first time and could serve as the background for the monitoring of possible heavy metal contaminations in the alligator habitats.