Kekkei Genkai ("Bloodline Limit") are genetic abilities passed down in specific family clans. Though they are not technically jutsu, most clans have developed their own jutsu that work with them, and will not work for those without the genetic trait.
 List of Kekkei Genkai
Main article: Byakugan
The Byakugan (lit. "White Eye") is a genetic eye condition that only occurs in members of the Hyuga (Hyūga) clan. Ninja with the Byakugan are characterized by having white, pupil-less eyes. When activated, the users pupils become more defined, and the veins near the temples bulge. The Byakugan grants the user clarity of perception; in some cases to a much higher degree than the Rinnegan and Sharingan. One of its unique abilities is that is can vividly view even the most minute objects from several meters away--its total range depending on the user. Furthermore, it grants a near 360 degree field of vision, allowing the user to see incoming attacks from almost all directions except for its one minuscule blind spot which is located behind the first thoracic vertebra. Finally, the Byakugan allows the user to see a person's chakra flow as well as the several chakra points (tenketsu) throughout the body.
Using the aforementioned ability, the Hyuga clan has developed the ability to forcibly release their chakra one of the opponent's 361 chakra points (tenketsu), ceasing chakra flow altogether or attacking internal organs directly. This method of fighting is called Gentle Fist (Jūken), named so because it involves little physical contact. In order to protect the secrets of the Byakugan and the Gentle Fist secret techniques, the Hyuga clan imposed a strict hierarchy by dividing the clan between the main family and the branch family. Members of the branch family are branded with the curse seal, which will destroy the Byakugan abilities in them when they die. Furthermore, they are also forbidden to learn the Gentle Fist secret techniques.
 Dead Bone Pulse
Dead Bone Pulse (Shikotsumyaku) is a genetic ability exclusive to members of the currently extinct Kaguya clan. This ability grants the user complete control of his/her skeletal structure and allows them to manipulate it in anyway they please. Moreover, their bones are several times harder and durable than the average human being and can repel even some of the sharpest objects. As demonstrated by Kimimaro Kaguya, the user can use their bones as a defense, a weapon, and even as a projectile that can pierce through tough objects.
 Ice Release
Ice Release (Hyōton, English TV: "Ice Style") refers to a new elemental type of ninjutsu exclusively available to Haku. It is achieved by combining water and wind natured chakra. Since he was a child, Haku has been able to create and manipulate ice with ease simply by using his willpower. The ice Haku creates is highly resistant to heat and fire, rendering fire techniques almost useless against it. Using this ability, Haku has developed a slew of techniques that use his ice release ability, including his most prominent one called Demonic Ice Crystal Mirrors.
Main article: Rinnegan
The Rinnegan (lit. "Samsara Eye") is recognized as the most powerful of the three eye techniques (dōjutsu) (the other two are the Sharingan and Byakugan). An activated Rinnegan is characterized by having blue eyes with several rings around the pupils. The primary ability the Rinnegan is known for is that it allows the user to cast all types of ninjutsu. It also seems to grant the user the ability to take control of deceased corpses and bring them to life, although little is known about that. Any other abilities the Rinnegan grants is currently unknown. Use of the Rinnegan seems to have no detrimental effect on the user, seeing how Nagato has it constantly activated. The first person known to possess the Rinnegan is the Sage of the Six Paths, who is also known to have given birth to ninjutsu and founded the entire ninja world. The only other person known to possess the Rinnegan is Nagato, a member of Akatsuki.
Main article: Sharingan
The Sharingan (lit. "Copy Wheel Eye") is an genetic eye condition that only occurs in members of the Uchiha clan. It doesn't appear at birth, but it is activated when the user is in a stressful situation in battle. It is rumored that the Sharingan descended from the Byakugan, although it grants different abilities and perceptions. The power of the Sharingan can be determined by the number of tomoe in each eye up to a maximum of three. The first and most well known ability is to read and memorize any technique. However, the user must be physically capable to perform copied techniques. Its ability grants the user extraordinary clarity of insight, allowing users to follow fast moving objects with ease and even predict the subsequent action of those objects. This awareness is also clear enough to see through illusions and the stream of chakra, but not to the same degree as the Byakugan. The third skill the Sharingan grants is the power of hypnosis which involves proposing thoughts and actions to a user's opponent. This skill used in conjunction with the aforementioned talents of the Sharingan can allow users to perfectly mimic the movements of his/her opponents even before they do as if they were seeing the future. The Sharingan also grants other forms of hypnotism, which includes putting people to sleep, replaying the memories of someone, creating illusions, and even controlling a person.
The only non-Uchiha Sharingan user is Kakashi, whose Sharingan eye was transplanted from Obito. Although it is possible to transplant Sharingan eyes, they do not function well in ninja who are not descendants of the Uchiha clan. The use of the Sharingan puts a strain on the user's chakra, which is why Kakashi is often extremely exhausted after extended use of the Sharingan. However, this chakra strain is insignificant in members of the Uchiha clan, so they can use the Sharingan extensively with relative ease. Itachi, for example, has his Sharingan activated almost constantly.
 Mangekyō Sharingan
The Mangekyō Sharingan (lit. "Kaleidoscope Copy Wheel Eye") is the heightened form of the Sharingan. The first users of the Mangekyō Sharingan is Madara Uchiha, the founder of the Uchiha Clan, who used it to take control of the nine-tailed fox, and his little brother Izuna Uchiha. Several generations later, only a handful of other ninja came to acquire their own Mangekyō Sharingan, starting with Itachi, then Kakashi, and finally Sasuke. They and Madara are currently the only ones in the Naruto storyline who possess the Mangekyō Sharingan. Unlike a regular Sharingan, the Mangekyō Sharingan's is unique between users, drastically changing the form of the Sharingan's tomoe seals when activated.
The Mangekyō Sharingan, despite granting the user great power, has one grave flaw--it deteriorates the user's normal eyesight. Extensive or repeated use of the Mangekyō Sharingan will hasten the deterioration process until the user ultimately becomes blind. However, Madara, after realizing this drawback, found a way to permanently restore his eyesight by transplanting the eyes of his little brother into his own sockets. In doing so, Madara came to possess a permanent Mangekyō Sharingan devoid of its original weaknesses in addition to incredible power.
When the Mangekyō Sharingan is initially unveiled, Itachi tells Sasuke that the only way to obtain it is by killing one's closest friend. However, it can be inferred that one doesn't necessarily have to kill his closest friend; Kakashi was able to obtain his Mangekyō Sharingan in this manner since his former teammates are both dead.