Registration numbers have only ever been provided within the supplementary databooks of the Naruto series, and even then only for characters that are given full biographies. Some such characters have their registration numbers listed as "?", implying that they have one but that it is not being disclosed for whatever reason; Minato Namikaze is initially listed in this way before a proper number is provided in Jin no Sho. Still other characters have registration numbers listed as "—", implying they do not have one at all, either because their village does not use registration numbers (discussed below), because the character became a ninja before their respective village was founded (such as with Hashirama Senju and Ōnoki), or for some other unknown reason (as with the Ame Orphans and Iwagakure's jinchūriki).
Registration numbers are used by all of the villages of the Five Great Shinobi Countries with the exception of Kirigakure, whose ninja have consistently been listed without one. Of the smaller villages, only Amegakure is known to use registration numbers. Ninja of Otogakure (as with Team Dosu in Rin no Sho), Yugakure (as with Hidan in Sha no Sho), and Takigakure (as with Fū in Jin no Sho) are listed without registration numbers, suggesting those villages do not use them. Only two ninja from Uzushiogakure have ever received full biographies in the databooks: Mito Uzumaki is listed without a registration number, though this may be because of her age; Kushina Uzumaki is listed with a registration number, though it conforms to the numbering scheme used by Konohagakure, where she received her ninja training. Thus, it's unclear whether or not Uzushio used registration numbers at any point. Ninja from Kusagakure have never received full biographies, again making it unclear if the village uses them.
Beyond the existence of ninja registration numbers, the databooks never go into detail about them, rendering everything that can be said about them entirely observational. Individuals evidently receive their numbers when they complete their ninja training, most commonly by graduating from their village's Academy: twenty-seven students graduate from Naruto Uzumaki's Academy class, though only nine of those students are ultimately accepted as genin. Those nine graduates have registration numbers ranging from 012601 to 012625, with the unaccounted for intervening numbers presumably belonging to the eighteen graduates who were denied as genin. Accordingly, members of genin teams generally have registration numbers within close proximity of each other, sometimes even consecutive numbers: the Sannin are numbered 002300, 002301, and 002302. With the exception of Amegakure, registration numbers are seemingly assigned sequentially, so that new ninja will receive higher numbers than their predecessors: Konohamaru Sarutobi is numbered 012707, while his grandfather is numbered 000261; Gaara is numbered 56-001, while his sister (three years his senior) is numbered 53-004.
Because ninja registration numbers roughly correspond to a character's age, all characters with "?" listed as their registration number are likewise not listed with ages in the databooks. Examples include Pakura, Gari, and the Third Raikage.
Similarly, when Iruka Umino's age is reduced from 25 in Rin no Sho to 23 in Tō no Sho, his registration number is changed as well, going from 011450 in the former to 011850 in the latter.
Several characters with "—" listed as their ninja registration numbers are similarly listed without ninja ranks, potentially explaining why they did not receive numbers. Examples include Karura, Rōshi, and Nagato.