Hidden villages generally have a hierarchy made up of ranks for their shinobi. Though the exact structure varies from village to village, the main ranks generally remain the same. At the top of the chain is the Village Head; in the case of the Five Great Shinobi Countries, the village head is given the title of Kage. The shinobi are lead by the head, though the higher-ranking ones may assist them in leading the village.
- Academy students (忍者学校生, Akademī-sei) are students of the village's academy. They are not considered official shinobi, but rather, shinobi-in-training. As such, they do not partake in missions. Instead, they are taught by academy teachers about shinobi life, and are taught the bare basics of chakra usage, ninjutsu and taijutsu. Their fighting capabilities are low and undeveloped, as the academy is where they learn basic sparring tactics.
- Genin (下忍; Literally meaning "junior ninja") is the lowest rank of the shinobi, given to one once they graduate from the academy. A genin will be assigned to two others in a squad and given a squad leader of chūnin rank of above. The squad will complete missions together, though as they are new genin their tasks will rarely involve fighting, and nothing that will put them at serious risk unless they show real potential.
- Chūnin (中忍; Literally meaning "Journeyman Ninja") are the next rank up. Shinobi of this rank are considered to be more mature and show leadership qualities. Because of this, they may be able to take on missions without squads, and may begin to take on more dangerous missions. Chūnin are also often given their village's flak jacket to differentiate them from genin.
- Tokubetsu Jōnin (特別上忍; Literally meaning "Special High Ninja") is the rank between chūnin and jōnin. They are shinobi that demonstrate jōnin-level skill in a particular field, as opposed to all-round skill. Tokubetsu Jōnin do not always go on missions reserved for those of jōnin rank (though almost all are at chūnin rank in terms of general skill), but rather assist the village by putting their advanced skill to daily use.
- Jōnin (上忍, Jōnin; Literally meaning "High Ninja") is the highest rank most shinobi will achieve. They are shinobi that have proven their worth over the course of years, and are very skilled in their work. They are sent on the highest-ranking missions, and may also be assigned a squad of genin to train.
- The Village Head (里長, sato-osa) is the administrative and military leader of the village. They are always a shinobi that has proven them self as one of the strongest in their village in order to demonstrate the village's power to the other countries. The Village Head of a village of the Five Great Shinobi Countries is refereed to as a Kage (影; Literally meaning "Shadow").
The medical teams (医療班, Iryō-han) are groups made up of medical-nin. Like Tokubetsu Jōnin, they are less likely to be found on the battlefield. Instead, they work behind the scenes or in the village hospital, tending to the wounds of injured shinobi. They too are shinobi, and are also capable of holding their own in a fight, but because their priority is supporting their team and healing the injured, they rarely take on the offensive. Their techniques are also more focused around treating injuries, both through usual means and chakra. They continuously work to create new advances in medical technology.
The ANBU(暗部; Literally meaning "Dark Side"), short for Ansatsu Senjutsu Tokushu Butai (暗殺戦術特殊部隊; Literally meaning "Special Assassination and Tactical Squad"), are shinobi that take orders directly from their Village Head or Kage. They are generally known as shinobi that specialise in 'Black Operations' such as torture and assassination. Because they are used for such secret missions, the members of ANBU are hand-picked by the village leader. Even in their village they wear masks whilst on duty, hiding their identity from those outside the squad.