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- bka' brgyud sngags mdzod, a collection of the most important empowerments, practices and instructions of the Kagyu lineages, in 8 volumes.
- gdams ngag mdzod, a collection of empowerments, practices and teaching of all eight major lineages of Tibet, in 18 volumes.
- rin chen gter mdzod, a collection of terma (gter ma) teachings of the 100 major treasure revealers (gter ston) of Tibet, in 63 volumes.
- shes bya kun khyab mdzod, Jamgon Kongtrul's famous encyclopedia of buddhism and buddhist culture, in 3 volumes.
- rgya chen bka' mdzod, a collection of all the writings by Jamgon Kongtrul himself, in 17 volumes. The shes bya kun khyab mdzod is often included in this collection which then has 20 volumes.
- "The Dam Ngak Dzod is one of the five great treasuries composed by first Jamgon Kongtrul Rinpoche. These are:
- Sheja Kunkhyen Dzod:- a commentary of the whole buddhist path including art, history, doctrine, etc and structured according to the views of Hinayana, Mahayana and Vajrayana.
- Kagyu Ngak Dzod: a collection of Marpa’s teaching about the formal knowledge of ritual, iconography etc. the Shegyuin teachings. It is necessary for an-impeded continuation of the empowerments. The Segyuin teachings Marpa, the translator, transmitted to three foremost disciples and were scattered in many subschools and traditions. The Drubgyuin which guides the disciple to perfection in his practice had transmitted totally to Milarepa, the Tibet’s Great Yogi.
- The Rinchen Ter Dzod, a compendium of Nyingmapa teachings transmitted by Guru Rinpoche through revelation of spiritual treasures too much later masters.
- Dam Ngak Dzod: a collection of the essential teachings of the eight practice lineages of Tibetan Buddhism.
- Thumong Ma- yinpa Dzod: which represents Kongtrul Rinpoche’s own writings which are included in the other treasuries.