He is the son of Craster, a wildling who marries his daughters, and Gilly, one of his daughter-wives, being his mother/half-sister. He was named after Samwell Tarly, who saved the lives of Gilly and her son. Later Tarly secretly adopted Sam, presenting the boy as his bastard son and of his blood.
Two of Craster's wives deliver Gilly's baby in a birthing hut. At the same time the Night's Watch survivors of the Battle of the Fist of the First Men take shelter at Craster's Keep. After Gilly and Samwell Tarly notice that her new baby is a boy, they realize that Craster will want to sacrifice him to the White Walkers.
Sam visits Gilly, who is deeply distraught about the impending fate of her newborn son. She is frantic, and yells at Sam not to draw attention to his gender, as Craster will want to offer it up as a sacrifice when he finds out. He asks her if she has decided on a name, but she responds that there is no point in naming her baby if he is only going to be offered up as a human sacrifice. She gives Sam back his mother's thimble and says she doesn't care about such stupid things, and is focused only on protecting the life of her baby.
When a mutiny breaks out that results in the deaths of Craster and Lord Commander Jeor Mormont, Sam rushes to Gilly's hut and tells her that they must leave. Sam runs out of Craster's Keep with Gilly and her baby, as loyal Night's Watch members fall to the mutineers, who also kill or rape Craster's other wives. Gilly leads the way into the night because she knows the woods around her home.
After several days of travelling, Sam, Gilly, and her baby arrived at an abandoned cabin in a forest. After lighting a fire, Sam suggests that Gilly name her son but she does not know any boy names. Sam gives her some examples, and also explains the difference between first and last names. They are interrupted by the squawks of several crows outside. When Sam and Gilly, who is carrying the baby, went out to investigate, they saw hundreds of crows squawking angrily at them. Shortly later, Gilly witnesses a White Walker approaching and realized that the creature has come for the baby due to Craster's habit of sacrificing male babies to these creatures. Sam manages to kill the White Walker with a dragonglass dagger. The three of them then flee into the night.
Following their encounter with the White Walker, Sam's mother Gilly and her protector Samwell continue their journey to Castle Black, the headquarters of the Night's Watch. Based on Samwell's knowledge of the roads and places in the North, they head for Nightfort, an abandoned castle which was formerly the headquarters of the Night's Watch and is situated between Castle Black and Beyond the Wall. After travelling past the Wall, Sam and the adults finally reach Nightfort, where they encounter Bran Stark, the half-brother of Samwell's friend Jon Snow. Bran and his companions—Jojen Reed and his sister Meera, the servant Hodor and the direwolf Summer are travelling Beyond the Wall in search of the three-eyed raven.
Due to their experiences beyond the Wall, Samwell and Gilly are not willing to return to the Wall with Bran and company. They part company, and Sam and the adults complete their journey to Castle Black. There, they met Maester Aemon, who is furious at the prospect that Samwell has violated his vows. However, Aemon's demeanor softens upon learning that Gilly was one of the late Craster's wives and that Sam is one of his offspring. Aemon acknowledges that Gilly is now a refugee and that she and her child should be sheltered since the North is no longer safe for humans. Aemon then orders Sam to begin writing letters immediately and to make sure that all forty-four of Castle Black's ravens are well-fed, as every one of them will fly that night: the White Walkers have returned, and Westeros must be warned. For the moment, Sam and his mother are safe from the White Walkers.
Worried about Gilly and her baby, Samwell Tarly has them sent away to Mole's Town. Gilly is given work at the local brothel.
A whore is annoyed that Gilly's baby woke her up during a night in Mole's Town. Meanwhile, a wildling raiding party, including Tormund, Styr, and Ygritte, attack the town, killing everyone in their path. Ygritte discovers Gilly hiding with her baby, but urges them to keep quiet, sparing their lives.
Gilly and her baby flee to the safety of Castle Black. Sam is overjoyed to see them and has them hide in a storage room for the duration of the battle.
Little Sam remains with his mother Gilly at Castle Black. However, Gilly is fearful that she and her baby may be sent away if Ser Alliser Thorne is chosen as the new Lord Commander of the Night's Watch.
On his deathbed, Maester Aemon fondly interacts with Little Sam, recalling that his younger brother Egg had a jolly laugh just like him when he was a baby. His strength failing, he also warns Gilly that she must go south with her baby before it is too late - winter is almost upon them and the White Walkers will come with it to attack the Wall.
Sam asks Jon if he can travel to Oldtown to study and replace Aemon as the new maester for Castle Black, as he feels there is no other way he can help them as he cannot fight. He also wishes to take Gilly and little Sam with him, in order to protect them from the coming war against the White Walkers. Jon allows this and Sam, Gilly and little Sam depart shortly after.
Little Sam accompanies his mother Gilly and Samwell Tarly on a sea voyage to Oldtown in The Reach. Since the Citadel only admits men within its walls, Samwell plans to send Sam and his mother to live with his family at Horn Hill. Samwell is unwilling to abandon Sam and his mother to the tender mercies of the streets of Oldtown.
After landing in Oldtown, Little Sam, Gilly, and Samwell travel by station coach to the Tarly family home at Horn Hill. To protect Gilly, Samwell claims that she was a Northern woman he had bedded in Mole's Town and that Little Sam is his son. Upon arriving at Horn Hill, Sam and the adults are welcomed by Samwell's mother Melessa and his sister Talla Tarly, the former of whom Sam seems to like. While Melessa and Talla are friendly and hospitable, Samwell's father Randyll Tarly is hostile and derides Sam's mother for being a Wildling. Later that night, Samwell steals the family heirloom Heartsbane and flees Horn Hill with both Gilly and Little Sam.
After arriving in Oldtown, Sam and Gilly meet a Citadel maester. Sam gives him a letter from Lord Commander Snow about Sam becoming a maester for the Night's Watch, but the maester is skeptical about Jon Snow's state, saying that no word was given about Lord Commander Mormont's death from Maester Aemon. The maester states that Sam's situation is "irregular" to which Sam responds, "Life is irregular." The maester then says that Sam must speak to the Archmaester in order to discuss these issues. The maester then allows Sam to use the library, but blocks Gilly and Little Sam from entering.
A child of incest, sam's brothers were sacrificed to White Walkers by his father Craster. During the Night's Watch mutiny at Craster's Keep, Gilly escaped with Samwell Tarly and her newborn son. Sam took care of the boy as his own, prompting Gilly to name the babe after him. With his parents, baby Sam has arrived at Oldtown.