Although the Daigokuden is depicted as a single storey building in "Nenju Gyoji Emaki" and "Heian Tsushi" (the history of Heian-kyo) compiled by the Counselor for Kyoto City in 1895, the original building had most likely been a two-storey massive structure comparable to Todai-ji Temple Daibutsuden (the house of the Great Buddha) in Nara or Izumo-taisha Shrine, as the expression 'Unta (Izumo taisha-Shrine as first), Wani (Todai-ji Temple Daibutsuden as second), and Kyosan (Heian-kyo Daigokuden as third)' is found in "Kuchizusami" (folk poems) written in 970, because the main building of the Daigokuden was rebuilt twice following two fires, and "Nenju Gyoji Emaki" depicts the Daigokuden rebuilt in 1072.
なお、『年中行事絵巻』や、1895年（明治28年）京都市参事会によって編纂された『平安通志』には、単層の大極殿が描かれているが、大極殿殿舎は火災により2度も建て替えられており、970年（天禄元年）成立の『口遊（くちずさみ）』に「雲太、和二、京三」と見えるように、当初は出雲大社や奈良の東大寺大仏殿に匹敵する大建築であり、『年中行事絵巻』所載のものは1072年（延久4年）に建て替えられた姿で、本来は重層（2階建て）であったとも推測される。