Ninja is the on'yomi reading of the two kanji 忍者 used to write shinobi-no-mono (忍の者), which is the native Japanese word for people who practice ninjutsu (sometimes erroneously transliterated as ninjitsu 忍術). The words: ninja and shinobi-no-mono, along with shinobi, another variant; became popular in the post-World War II culture. The term shinobi (historically sino2bi2 written with the Man'yōgana 志能備), has been traced as far back as the late 8th century when Heguri Uji no Iratsume wrote a poem  to Ōtomo no Yakamochi. The underlying connotation of shinobi (忍), in Sino-Japanese means "to steal away" and—by extension—"to forbear," hence its association with stealth and invisibility. Mono (者, likewise pronounced sha or ja) means "person." The nin of ninjutsu is the same as that in ninja, whereas jutsu (術) means skill or art, so ninjutsu means "the skill of going unperceived" or "the art of stealth"; hence, ninja and shinobi-no-mono (as well as shinobi) may be translated as "one skilled in the art of stealth." Similarly, the pre-war word ninjutsu-zukai means "one who uses the art of remaining unperceived."
Other terms which may be used are oniwaban (お庭番 "one in the garden", suppa, rappa, mitsumono, kusa (草 grass) and Iga-mono (one from Iga).
In English, the plural of ninja can be either unchanged as ninja, reflecting the Japanese language's lack of grammatical number, or the regular English plural ninjas.
 Historical period of origin
The ninja use of stealth tactics against better-armed enemy samurai does not mean that they were limited to espionage and undercover work: that is simply where their actions most notably differed from the more accepted tactics of samurai. Their weapons and tactics were partially derived from the need to conceal or defend themselves quickly from samurai, which can be seen from the similarities between many of their weapons and various sickles and threshing tools used at the time. .
Ninjas as a group first began to be written about in 15th century feudal Japan as martial organizations predominately in the regions of Iga and Koga of central Japan, though the practice of guerrilla warfare and undercover espionage operations goes back much further.
At this time, the conflicts between the clans of daimyo that controlled small regions of land had established guerrilla warfare and assassination as a valuable alternative to frontal assault. Since Bushido, the Samurai Code, forbade such tactics as dishonorable, a daimyo could not expect his own troops to perform the tasks required; thus, he had to buy or broker the assistance of ninja to perform selective strikes, espionage, assassination, and infiltration of enemy strongholds (Turnbull 2003).
There are a few people and groups of people regarded as having been potential historical ninja from approximately the same time period. It is rumored that some of the higher-ranking daimyos and shoguns were in fact ninja, and exploited their role as ninja-hunters to deflect suspicion and obscure their participation in the 'dishonorable' ninja methods and training.
Though typically classified as assassins, many of the ninja were warriors in all senses. In Hayes's book, Mystic Arts of the Ninja, Hattori Hanzo, one of the most well-known ninja, is depicted in armor similar to that of a samurai. Hayes also says that those who ended up recording the history of the ninja were typically those within positions of power in the military dictatorships, and that students of history should realize that the history of the ninja was kept by observers writing about their activities as seen from the outside.
"Ninjutsu did not come into being as a specific well defined art in the first place, and many centuries passed before ninjutsu was established as an independent system of knowledge in its own right. Ninjutsu developed as a highly illegal counter culture to the ruling Samurai elite, and for this reason alone, the origins of the art were shrouded by centuries of mystery, concealment, and deliberate confusion of history" The Historical Ninja. --By Sōke Masaaki Hatsumi
A similar account is given by 10th dan instructor Stephen K. Hayes, who was the first American to be accepted as a student by Grandmaster Hatsumi-- "The predecessors of Japan's' ninja were so called rebels favoring Buddhism who fled into the mountains near Kyoto as early as the 7th century A.D. to escape religious persecution and death at the hands of imperial forces" Ninjutsu: The Art of Invisibility.
 Historical organization
In their history, ninja groups were small and structured around families and villages, later developing a more martial hierarchy that was able to mesh more closely with that of samurai and the daimyo. These certain ninjutsu trained groups were set in these villages for protection against raiders and robbers.
While ninjas were limited exclusively to males, "ninja museums" in Japan declare women to have been ninjas as well (Turnbull 2003). A female ninja may be kunoichi (くノ一); the characters are derived from the strokes that make up the kanji for female (女). They were sometimes depicted as spies who learned the secrets of an enemy by seduction; though it's just as likely they were employed as household servants, putting them in a position to overhear potentially valuable information. 
As a martial organization, ninja would have had many rules, and keeping secret the ninja's clan and the daimyo who gave them their orders would have been one of the most important ones..
For modern hierarchy in ninjutsu, see: Ninjutsu
 Historical garb, technique, and image
There is no evidence that historical ninja limited themselves to all-black suits. In modern times, camouflage based upon dark colors such as dark red and dark blue can be used to give better concealment at night. Some cloaks may have been reversible: dark colored on the outside for concealment during the night, and white colored on the inside for concealment in the snow. Some ninja may have worn the same armor or clothing as samurai or Japanese peasants.
The stereotypical ninja that continually wears easily identifiable black outfits (shinobi shozoku) comes from the Kabuki theater.  Prop handlers would dress in black and move props around on the stage. The audience would obviously see the prop handlers, but would pretend they were invisible. Building on that willing suspension of disbelief, ninja characters also came to be portrayed in the theater as wearing similar all-black suits. This either implied to the audience that the ninja were also invisible, or simply made the audience unable to tell a ninja character from many prop handlers until the ninja character distinguished himself from the other stagehands with a scripted attack or assassination.
Ninja boots (jika-tabi), like much of the rest of Japanese footwear from the time, have a split-toe design that improves gripping and wall/rope climbing. They are soft enough to be virtually silent. Ninja also attached special spikes to the bottoms of the boots called ashiko.
The actual head covering suggested by Sōke Masaaki Hatsumi (in his book The Way of the Ninja: Secret Techniques) utilizes what is referred to as sanjaku-tenugui, (three-foot cloths). It involves the tying of two three-foot cloths around the head in such a way as to make the mask flexible in configuration but securely bound. Some wear a long robe, most of the time dark blue (紺色 kon'iro) for stealth.
 Associated equipment
The assassination, espionage, and infiltration tasks of the ninja led to the development of specialized technology in concealable weapons and infiltration tools.
 Specialized weapons and tactics
Ninja also employed a variety of weapons and tricks using gunpowder. Smoke bombs and firecrackers were widely used to aid an escape or create a diversion for an attack. They used timed fuses to delay explosions. Ōzutsu (cannons) they constructed could be used to launch fiery sparks as well as projectiles at a target. Small "bombs" called metsubushi (目潰し, "eye closers" were filled with sand and sometimes metal dust. This sand would be carried in bamboo segments or in hollowed eggs and thrown at someone, the shell would crack, and the assailant would be blinded. Even land mines were constructed that used a mechanical fuse or a lit, oil-soaked string. Secrets of making desirable mixes of gunpowder were strictly guarded in many ninja clans.
Other forms of trickery were said to be used for escaping and combat. Ashiaro are wooden pads attached to the ninja's tabi (thick socks with a separate "toe" for bigger toe; used with sandals). The ashiaro would be carved to look like an animal's paw, or a child's foot, allowing the ninja to leave tracks that most likely would not be noticed.
Also a small ring worn on a ninja's finger called a shobo would be used for hand-to-hand combat. The shobo (or as known in many styles of ninjutsu, the shabo) would have a small notch of wood used to hit assailant's pressure points for sharp pain, sometimes causing temporary paralysis. A suntetsu is very similar to a shobo. It could be a small oval shaped piece of wood affixed to the finger by a small strap. The suntetsu would be held against a finger (mostly middle) on the palm-side and when the hand that was thrust at an opponent, the longer piece of wood like the size of ones larger arm would be used to hit the pressure points such as the solar plexus.