We investigated glacier changes in the Karatal river basin, the largest basin in Zhetysu (Dzhungar) Alatau, Kazakhstan, for the periods 1956–89, 1989–2001 and 2001–12, based on Landsat TM/ETM+ data analysis. In 1989, we found 243 glaciers with a total area of 142.8 km2; by 2012 these had shrunk to 214 glaciers with a total area of 109.3 km2, a decrease of 33.5 km2 over 23 years (1.02%a-1). This very high shrinkage rate is likely connected with a general trend of increasing temperatures, and small glaciers being situated at the relatively low altitude of the outer Zhetysu Alatau ranges. We also analyzed the shrinkage rate of glaciers based on their differences in size, altitude and aspect of slopes, as well as other topographic parameters, in four sub-basins where glacier shrinkage varied between 18% and 39%. Weather-station climate data showed a significant temperature increase and stable precipitation trends over the study period. We conclude that glacierized areas of the Karatal river basin are located in the most unfavorable conditions for glaciation, and as a result showed a higher shrinkage rate than other glacierized areas of the Tien Shan from 1956 to 2012.