The handwritten copies such as the one owned once by the Kujo family and currently by the Imperial Household Archives, Vol. 5 of the Chokyu Gannen Ki (chronicle of the first year of the Chokyu era) in the Kamakura period, the one possessed by Kaku TANAKA, Vol. 1 of the Choreki Ninen Ki (chronicle of the second year of the Choreki era), and the one owned by Sonkeikaku-bunko library, Vol. 3 of the Eisho Sannen Ki (chronicle of the third year of the Eisho era) in the Sanjonishike-bon (Sanjonishi family book) include many entries that are not contained in the Toji-bon.
鎌倉時代書写の書陵部所蔵の九条家旧蔵本長久元年記5巻・田中穫所蔵本の長暦2年記1巻・尊経閣文庫所蔵の三条西家本永承3年記3巻には、東寺本には収録されていない月日も多く含んでいる。