Major themes in Shiloh include justice, and determining what is right or wrong, and the importance of family and friends. Naylor used her personal experience — finding a silent, skinny, scared dog while taking a walk in West Virginia — to convey the notion that a person's perspective changes when he or she becomes emotionally involved in a problem.
The first time Marty whistles and Shiloh runs to him, wagging his tail, licking Marty's fingers and face, Marty's perspective about what is best for Shiloh becomes subjective. Marty becomes emotionally involved with Shiloh; he "got hooked on him." Marty's perspective causes him to feel responsible for Shiloh's welfare, even though Shiloh belongs to Judd Travers. Marty faces a moral dilemma that involves justice. He has to make a decision about what is right and what is wrong, and then act on his decision. In Marty's situation, the decision is not clear-cut. He hides Shiloh and keeps Shiloh's presence a secret from everyone. He struggles with knowing that he is doing what he thinks is best for Shiloh, but he is being dishonest with his family and with his good friend, David Howard. Marty feels guilty about the lies that he tells to protect Shiloh; however he justifies his lies because he truly believes that caring for Shiloh is what Jesus would want him to do. He prays to Jesus asking, "Which you want me to do? Be one hundred percent honest and carry that dog back to Judd so that one of your creatures can be kicked and starved all over again, or keep him here and fatten him up to glorify your creation?" To Marty, "a lie don't seem like a lie anymore when it's meant to save a dog." Life becomes complicated for Marty. He is being pulled in several different directions. He doesn't know what the boundary is between living strictly according to the law (which would mean giving Shiloh back to Judd because Judd legally owns Shiloh) or living according to what he feels is the right thing to do (protect Shiloh from Judd's abuse). Marty loves his family and has never lied to them before, but now, he also loves Shiloh.
Marty must figure out what to do based on his own sense of right and wrong, taking into consideration his family's values. Marty questions his parents by asking, "What kind of law is it . . . that lets a man mistreat his dog?" and "What's right?" Naylor points out that there are exceptions to every rule and that it is necessary throughout life to stand up for what you believe is fair and just and then be ready to compromise. Marty does compromise — using time to figure out how he can keep Shiloh. He agrees to take Shiloh back to Judd after Shiloh is well. Later, Marty also compromises with Judd. Marty agrees to work for Judd and keeps quiet about the fact that Judd shot a deer illegally in exchange for Shiloh. Throughout the process, Marty realizes that "nothing is as simple as you guess — not right or wrong. . . ."
Another major theme in Shiloh is the importance of family and friends. Family is a priority for the Prestons. Even though they don't have much money, they manage to send money to help Aunt Hettie care for Grandma Preston. When Marty goes on the postal route with his father, his father shows that he cares about Marty and has been paying attention to him by asking Judd questions about his dogs. Marty's father knows Marty is worried about Shiloh and he seems to know what to ask Judd to satisfy Marty's interest. When Marty's family discovers his secret (Shiloh) and realizes he has been lying to them, they are not happy about the lies, but they support him and assist him in righting a wrong. His parents stand beside him as he tells Doc Murphy and Judd the truth.
Marty's relationship with his friend, David, is also significant. Marty chose not to share his secret about Shiloh with David. When David did find out, he supported Marty and helped him clean out Shiloh's pen. Marty felt good having David's help because David's presence made the job easier and helped keep Marty from focusing on thoughts related to his guilt about the German shepherd attacking Shiloh. Marty thinks that he and David will be "friends for life." Being able to trust and depend on family and friends enables people to feel secure, thereby allowing each person in the relationship to flourish.
Naylor writes about the difficulties involved in deciding what is right and what is wrong and the value of family and friends to portray the notion that people are unique and naturally figure out solutions to life's dilemmas in their own way.