Ethnopharmacological relevance The Sowa-rigpa system of traditional healing has been practiced from time immemorial in western Ladakh but its existence is in jeopardy today. Documentation of information on various aspects of this system such as treatment methods, materials used for medicine and socio-cultural aspects is needed to ensure the long-term survival of this system. Materials and methods Extensive field surveys were conducted from March 2009 to June 2011 in three different Valleys of the Kargil district. Interviews with traditional healers, village heads and local people were conducted using semi-structured questionnaires and participatory observations to assess the current status of traditional medicine system. Plant specimens were collected from the field for identification and herbarium preparation which were later deposited in herbaria for future reference. Results 160 plants were recorded to be used by traditional healers of Western Ladakh. Traditional healing system (THS) is taking care of 30% of public healthcare. Only 36 traditional healers are left in this region of which 67% was found along the Wakha-chu Valley, followed by the Lower Indus Valley (17%) and the SuruValley (16%). The transfer of knowledge to the next generation is very low (25%) in Kargil. Low income and continuously deteriorating social status of healers has contributed to the decline of this system. Conclusions Lack of interest in young generation in adopting this system may pose a threat to the survival of Sowa-rigpa. Integration of this system with the modern healthcare system and more government support may prove effective to enhance its deteriorating conditions.