Neglected and underutilized food crops (NUFCs) have high nutritional value, but their role in achieving nutrition security is not adequately understood, and they do not feature in food and nutrition policies and programs of the countries of the Hindu-Kush Himalayan (HKH) region. Drawing examples from Pakistan and Nepal, this study investigates the importance of NUFCs in achieving nutrition security in the mountains and identifies key underlying reasons for the decline in their cultivation and use. The study found that the prevalence of malnutrition is significantly higher in the mountains than nationally in both Pakistan and Nepal and identifies the decline in the cultivation and use of micronutrient-rich NUFCs as one of the key reasons for this. The deterioration of local food systems, changing food habits, lack of knowledge about the cultivation, use and nutritional value of NUFCs and lack of attention to NUFCs in programs and policies are the key reasons for the abandoning of NUFCs by mountain communities. There is an urgent need to mainstream these crops into national programs and policies and to integrate them into local food systems. This will not only improve the nutrition security of mountain areas, but also biodiversity and local mountain economies.