In The Kite Runner, Ali probably knows that Hassan is not his son, but it is never stated and it also does not matter. For all intents and purposes, Hassan is his son. Ali loves Hassan as if he were his biological child, and Baba’s betrayal by sleeping with Sanaubar is never discussed.
There are clues along the way even before Rahim Khan tells Amir about Hassan’s lineage. For one thing, Baba seems too concerned about Hassan, more than he probably would if Hassan were just the son of a long-time loyal servant. For instance, Baba pays to have Hassan’s harelip surgically corrected. Also, Baba is heartbroken when Ali tells him that he and Hassan are leaving. If the reader notices these inconsistencies in Baba’s behavior, Ali probably does, too.
Nevertheless, Ali loves Hassan and stands up for him. He recognizes that his child would never steal the watch that is found in his drawer. Ali shows backbone when he tells Baba that they cannot stay in a situation in which the master of the house believes Hassan capable of stealing because Ali knows Hassan just as any father knows and understands his son. Although Ali is not Hassan’s biological father, he is so much more of a father to Hassan than Hassan's biological father is. Baba could have made Hassan’s life so much easier even if all he did for Hassan was teach him to read and write, but he never tried.
In chapter 17, Rahim Khan informs Amir that Hassan and his wife were violently murdered in the streets by ruthless Taliban soldiers, and Sohrab was taken to an orphanage in Karteh Seh. Rahim Khan then petitions Amir to travel to Kabul and bring Sohrab back to Pakistan, where he can be adopted by a loving Christian couple. Amir is astonished by Rahim Khan's request and refuses to go to Kabul. When Amir asks why Rahim has chosen him to save Sohrab, he responds by saying that they both know why it must be Amir. Rahim continues to try to persuade Amir to embark on the journey to save Sohrab, but Amir refuses to take the risk, which influences Rahim Khan to tell him the disturbing truth about his past.
Rahim elaborates on Ali's past relationship and mentions that he was unable to have a child with his first wife. Rahim then informs Amir that Ali was sterile, which means Baba was Hassan's biological father. The fact that Ali was aware that he was sterile implies that he knew Baba was Hassan's father all along. After not being able to have a child for three years, Ali would have known something was wrong and certainly suspect that Baba was Hassan's biological father. Ali would have also noticed the way Baba treated Hassan like a son. Even though Hosseini never explicitly states that Ali was aware that Baba was Hassan's biological father, it is certainly implied that he knew that Baba had betrayed...
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him and was Hassan's real father.
Chapter 18 gives readers further insight into the issue. After Amir leaves Rahim Khan's apartment, he angrily processes the information he's just learned and reflects on his past life from a different perspective:
The questions kept coming at me: How had Baba brought himself to look Ali in the eye? How had Ali lived in that house, day in and day out, knowing he had been dishonored by his master in the single worst way an Afghan man can be dishonored?
Though Rahim Khan does not directly tell Amir that Ali knew Hassan wasn't his son, this passage shows that, in retrospect, Amir believes that Ali must have known. While Amir is completely shocked by the news that Hassan was his brother, he is able to see, in retrospect, that many signs pointed that way his entire childhood. (In Chapter 18, Amir recalls Baba's insistence that he'd never get new servants, his quest to have Hassan's harelip fixed, and the way in which Baba "had wept, wept, when Ali announced he and Hassan were leaving us.")
Although Hosseini never directly writes that Ali knows about Hassan's true parentage, he implies that Ali most likely would have known. When Rahim Khan tells Amir the truth about Baba and Sanuabar's affair, he also tells Amir that Ali had been married before Sanuabar but that his first wife had left him for another man. While Ali's first wife had no children with him, she went on to have children with the other man. Ali is not stupid and most likely would have known that he was sterile and that Hassan could not have been his.
While this example does not necessarily mean that Ali would have known Baba was Hassan's father, Hosseini does give an example earlier in the book which implies that Ali knows Baba's secret. After a young Amir frames Hassan by hiding his new watch and money in Hassan's hut, Ali decides that he will not allow Hassan to endure any more cruelty. He tells Baba that he and Hassan can no longer live there, and Baba is devastated. When Baba begs Ali to stay, Ali adamantly refuses, and it is clear from the scene that Baba doesn't dare push him any further--Ali looks at Baba as if to remind him that Baba had already hurt him and Hassan enough. The only thing that would have caused this look is Ali's knowledge of Baba's betrayal with Sanuabar.