The characters in Motherless Brooklyn are both stock characters from hard-boiled detective fiction and parodied versions thereof. Frank Minna is a resourceful hood who recruits boys from St. Vincent's Home for Boys and transforms them into "Minna men," or crime apprentices. Frank is the father none of the boys have; he is their redeemer who gives them a new world to which they can belong: Brooklyn of the early 1970s. As Lionel puts it, "it was Minna who brought me the language, Minna and Court Street that let me speak." Like Lionel, Frank Minna delivers the puzzling language that makes the book operate. Frank has several signature phrases, including "wheels within wheels" which seems to refer to the "secret systems" that control Brooklyn, but could refer to a multitude of other social, psychological, and narrative systems as well. Another important line of Frank's is his advice to Lionel to "tell your story walking," advice which links not only storytelling and journeying, but storytelling and walking away. For Frank, telling one's story necessarily means leaving; he only has relationships with those who don't know his story. (Indeed, the story of Frank's life rather than his death is the true mystery of the novel.) In Motherless Brooklyn, Frank holds the secret knowledge that the boys desire: knowledge of his identity, knowledge of the true meaning of their work, the secrets of Brooklyn, knowledge of women, and secret knowledge of them, of who they are, reflected in his recognition of their worth. Frank himself is a mystery, however, one of the mysteries that Lionel must solve—the solution to the mystery that is Frank Minna leads, albeit in a circuitous route, to Lionel's solution of the mystery of his own identity. Although Frank is the boys' redeemer, Frank maintains his authority through secrecy. Frank is, finally, scared to reveal himself, scared of communication, as evidenced by his advice to stay with big-chested women because "a woman has to have a certain amount of muffling, you know what I mean? Something between you, in the way of insulation. Otherwise, you're right up against her naked soul." Lionel, on the other hand, as we have seen, overcomes this fear not only through communicating with other characters in the novel, but by communicating with us, the readers, by telling us his story.

Frank's widow, Julia, is probably the closest to a traditional hard-boiled detective novel character, a tough-talking dame out of a Raymond Chandler novel. And yet Julia, like many of the other characters, turns out not to be what she appears. She is, as revealed in the finale, a girl from Nantucket, seduced first by Gerard and his Eastern philosophy, and then by the books Frank read her: Spillane, Chandler, and Ross MacDonald, which provide her with both her identity and her language. The Minna men, too, seem to emerge from a hard-boiled detective novel. They are an odd group, assembled because they are different, not only from the other orphans, but from each other as well. Tony is the typical second-in-command of mob fiction and film; Danny is the hip, unreadable, impenetrable character of indeterminate race; and Gilbert is the bottom guy all hierarchies need, chosen simply because he is a thug.

Lionel shares attributes with other such hard-boiled heroes as Sam Spade and Philip Marlowe—he is alienated from the culture that surrounds him, detached, ironic, lawless, and cynical toward authority. Lionel can solve the crime, but cannot seriously disturb the criminal conspiracies he uncovers. And, like other detectives in hard-boiled fiction, Lionel is an anti-hero who battles both internal and external demons. Like Philip Marlowe and Sam Spade, Lionel stands for morality in an amoral world. Told in the first-person by an anti-hero narrator, Motherless Brooklyn suggests that the divisions between truth and appearance are not as simple as they may at first appear—and in a novel where there is a gap between the spoken word and its meaning (that is where consciousness itself is exposed as a gap) this division is made even more stark.