There are a few regions in the world where climate change might be as rapid as in the Himalayas, and even fewer where the consequences of climate change are likely to be as severe for biodiversity, ecosystems services and human well-being. The Himalayas, one of 34 global hotspots of biodiversity [1], and with about 15 000 glaciers—the highest concentration in the world—are a source of Asia’s eight largest rivers. More than 750 million people living in the Himalayas, and more than 1.4 billion inhabiting the river basins of the five major Asian rivers (Indus, Ganges, Brahmaputra, Yangtze and Yellow Rivers), are likely to face consequences of climate change occurring in the region [2]. Despite the immense likely environmental, economic and social costs of climate change, reliable information about the extent and magnitude of climate change and its consequences in the Himalayas are not well known. Indigenous knowledge held by local communities about climate change can benefit climate science and policy [3–5]. Recent studies on indigenous knowledge have examined perceptions about climate change [6–8] in Tibet, the Eastern Himalaya and the Western Himalayas [9–13], but those studies mostly report qualitative and descriptive results based on a small number of respondents, and do not examine impacts on biodiversity. Here, we report, for the first time, indigenous knowledge about climate change and its consequences for biodiversity and agriculture in the Himalayas using a large number of households. We address three questions: (i) what are the perceptions of local people about climate change in the Himalayas? (ii) How do the perceptions vary with the altitude? (iii) Are the perceptions consistent with scientific findings reported from diverse regions of the world?