Literary themes within the book include widespread references to senses (especially sight), the pursuit of truth in a gray world, the strength of friendship, and the importance of father-son bonds. Many themes common to Potok's works prevail such as weak women and children, strong father figures, intellectual characters, and the strength and validity of faith in a modern secular world. Potok accentuates the importance of silence, and its role as a medium of communication. Throughout the book, there are numerous instances where Danny and Reuven both receive and process information in a non-verbal form. Potok explicitly introduces this topic by alluding to the relationship between Danny and his father, where there is no verbal communication between them, except during religious study. The two-year-long silence between Danny and Reuven, imposed by Reb Saunders, is also rich in communicative interactions between the two friends; however, it effectively shows the constraints that silence can impose between individuals.
Another important theme is the contrast of tradition to modernity. Reb Saunders insulates and isolates himself from the modern world, including Modern Orthodoxy, in everything from the method used to study Talmud to the creation of the state of Israel. This struggle between holding on to the traditions of one's culture in an ever-changing world and taking on the culture of the adopted home country was also faced by Danny and Reuven, both of whom were raised in a different environment from their parents and have found themselves in such a situation. It reflects the struggle that many immigrants and their children experience after arriving in America.