The Valley of Horses is the second novel in the Earth's Children series by Jean M. Auel. This novel begins where Clan of the Cave Bear ended, with Ayla alone and searching for the Others. At the same time, the novel follows the adventures of two brothers, Jondalar and Thonolan, who are on a Journey together. When a cave lion Ayla befriended attacks Jondalar and Thonolan, Ayla is able to save Jondalar and nurse him back to health. With Jondalar, Ayla begins to learn about the people from whom she came and to discover the excitement of new love. The Valley of Horses continues Ayla's story in a new and exciting direction that brings Ayla acceptance of herself and a chance at love.

Ayla makes her way north, the direction Iza told her to go in order to find people of her own. Ayla travels so long that she becomes tired and decides to winter in a small valley she discovers nearly by accident. Ayla begins to gather food, killing her first large animal, and befriends a foal who, like her, has been left abandoned by her own kind. The first winter in her new valley is long and lonely, leaving Ayla too much time to dwell on all she has lost. The winter also gives Ayla too much time to think about her future and what might happen when she finds the Others. Ayla begins to wonder if they will accept her when the only people she ever knew could not. When Ayla adopts an injured cave lion her second summer alone, she finds another excuse not to continue her travels.

At the same time, Jondalar and Thonolan set out from the cave to go on a Journey together. The Journey begins with excitement when they come across a group of flatheads, animals they have heard stories about but never seen before. Later, they come into contact with a group of people not unlike themselves whose language they do not understand. Despite this barrier, it seems Jondalar's reputation as a gentle lover has proceeded him. The leader of these people want Jondalar to give First Rites of Pleasure to her great-great granddaughter with the hopes that the ceremony will give her a child of his spirit, with his blue eyes.

Jondalar and Thonolan move on, following the path of the Great Mother River. When they reach the place where the Sister River joins the Great Mother River, they are forced to find a safe way to cross the rivers. While they are struggling with this dilemma, Thonolan is gored by a rhino. Jondalar is unsure of what to do, running around in a panic, leaving bloody furs in strange places. One of these furs alerts a people down river who come to their rescue. Thonolan and Jondalar go to live with these people while Thonolan recovers. When Thonolan is well again, he finds that he has fallen in love with one of the women who helped with his care. Thonolan mates with this woman, content to spend the rest of his life with her people. Jondalar, devoted to his brother, decides to remain as well even though he is filled with a deep sense of homesickness for his home cave and his people.

Thonolan's wife, Jetamio, wants to have a child and continues to attempt to get pregnant despite several miscarriages. Finally Jetamio is able to carry a child to term. However, it soon becomes apparent that a childhood illness has left Jetamio unable to give birth. Jetamio dies. Thonolan is so consumed with grief that he cannot remain among Jetamio's people. Jondalar considers staying with the woman he has come to care for, but she sends him away, aware of his deep affection for his brother. Jondalar and Thonolan decides to finish the Journey they began together.

Jondalar quickly becomes aware that his brother is so sick with grief that he hopes to die. Jondalar tries to keep his brother safe, but when Thonolan goes into the den of a couple of cave lions, there is nothing Jondalar can do to save him. Ayla comes upon the den when she recognizes her cave lion's cries. Ayla saves Jondalar and takes him back to her cave. As Jondalar recovers from his wounds he teaches Ayla his language. Eventually Ayla is able to tell Jondalar about her past. Jondalar is disgusted with the idea that Ayla lay with a flathead and gave birth to his child. However, Jondalar overcomes his disgust as he quickly gets to know Ayla better. Soon they become lovers and Jondalar finds the love of a woman to the degree he has never known before.