The objective of this study is to reveal the isotopic composition of ice and meltwater in glaciated regions of South-Eastern Altai. The paper depicts differences between the isotopic composition of glacier ice from several types of glaciers and from various locations. Detected differences between the isotopic composition of glacier ice in diversified parts of the study region are related to local climate patterns. Isotopic composition of meltwater and isotopic separation for glacier rivers runoff showed that in the Tavan-Bogd massif, seasonal snow participates more in the formation of glacier runoff due to better conditions for snow accumulation on the surface of glaciers. In other research areas pure glacier meltwater prevails in runoff.