This work aimed to refine the Moderate Resolution Imaging Spectroradiometer (MODIS) based snow cover algorithm for the Hindu Kush-Himalayan (HKH) region. Taking into account the effect of the atmosphere and terrain on the satellite observations at the top of the atmosphere (TOA), particularly in heavily rugged Tibet plateau region, the surface reflectances were retrieved from the TOA reflectances after atmospheric and topographic corrections. To reduce the effects of the snow/cloud confusion, a normalized difference cloud index (NDCI) model was proposed to discriminate snow/cloud pixels, apart from use of the MODIS cloud mask product MOD35. Furthermore, MODIS land surface temperature (LST) product MOD11_L2 have been used to ensure better accuracy of the snow cover pixels. Comparisons of the resultant MODIS snow cover with those obtained respectively from high resolution Landsat ETM+ data and the MODIS snow cover product MOD10_L2 for the Mount Everest region at different seasons, showed overestimation of the MOD10_L2 snow cover with the differences of 50%, whereas the improved algorithm can estimate the snow cover for HKH region more precisely with absolute accuracy of 90%.