Glaciers are an important element of the environment in the source regions of the Yangtze and Yellow rivers on the Tibetan Plateau. Using Geographical Information System techniques, we have studied changes in the location of glacier margins in two areas: the Geladandong area in the headwaters of the Yangtze, and the A’nyêmaqên Shan mountains in the headwaters of the Yellow River. Marginal positions during the Little Ice Age (LIA) maximum, in 1969 in the Geladandong area, in 1966 in the A’nyêmaqên Shan, and in 2000 in both areas, were determined using aerial photographs, satellite images, topographical maps and digital elevation models. Extrapolating the results to the entire source regions of the Yangtze and Yellow rivers, we estimate that the total glacierized area decreased about 1.7% between 1969 and 2000 in the Geladandong area and about 17% between 1966 and 2000 in the A’nyêmaqên Shan. Glaciers were stable or advanced slightly between 1969 and 1995 in the Geladandong area, and between 1966 and 1981 in the A’nyêmaqên Shan, but have retreated since the mid-1990s in the former and since the 1980s in the latter. Significant increases in summer air temperature and decreases in annual precipitation are the causes of the present retreat. As a consequence of the retreat, water storage, as ice, in the Yangtze and Yellow river drainages is decreasing by 65–70 × 106 m3 a−1.