A ninja organization would be headed by a jōnin literally high ninja. Under jōnin would be several chūnin lit. middle ninja. Under chūnin would be several genin lit. low ninja. Upon receiving a mission from daimyō, the jōnin would use the chūnin to select necessary personnel from among the genin.

Some ninja groups would be smaller and may have been less structured. Other groups may have been structured more like an army and the leader may instead have been called shō or general.

While ninja are often depicted as male, females were often ninja as well. A female ninja may be called kunoichi; the characters are supposedly derived from the strokes that make up the kanji for woman.Though sometimes depicted as experienced prostitutes who learned the secrets of an enemy by seduction, they rarely used that method.