A post-earthquake survey was performed on Joglo Javanese wooden houses, seriously affected by the May 27, 2006 Yogyakarta earthquake in Java, Indonesia. Investigations on 20 damaged Joglo buildings reveal that the structure's damage can be classified into 3 categories: slip between columns and stone foundation, broken joints between outer ring beam and column, and collapse of core structure. Four damage levels were defined: I) damage on the base joint of side structure, II) fatal damage on the side-structure, III) destroyed core structure, and IV) totally collapsed core structure. The side structure turns out to be relatively weak, while the core structure is able to secure the structural performance of Joglo buildings. A distinct relationship was identified between the levels of structural damage and the area ratio of core structure and the main column projection. It was verified that structural proportion significantly contributes to the assessment of damage. The joint failure represents a significant point in terms of maximum retention for conservation. Based on a damage level approach, an assessment methodology to optimize reinforcing strategies. This paper gives recommendations for the preservation of such precious structures from future earthquakes, while avoiding inappropriate interventions.