Koestenbaum's work, both in poetry and nonfiction, has explored the social and mental life of American queer intellectuals. His best-known critical book, The Queen's Throat, is a rigorous exploration of a phenomenon frequently discussed casually but seldom considered from a scholarly viewpoint: the predilection of gay men for opera. Koestenbaum's claim is that opera derives its power from a kind of physical sympathy between singer and audience that has as much to do with desire as with hearing. He says of the act of listening:

The dance of sound waves on the tympanum, and the sigh I exhale in sympathy with the singer, persuade me that I have a body...if only by analogy, if only a second-best copy of the singer's body. I'm a lemming, imprinted by the soprano, my existence an aftereffect of her crescendo. (42)

Koestenbaum's conclusion is that gay men's affinity for opera tells us as much about opera and its inherent questions about masculinity as it does about homosexuality.

In Hotel Theory, a critical discussion of the meaning of hotel life, and the aesthetic implications of such isolation, runs concurrently with a fictionalised account of a hotel encounter between Liberace and Lana Turner.

Koestenbaum's poetry is often more measured than his criticism. It frequently comments on itself...on the disorderly process of poetry...as in "Men I Led Astray" (from The Milk of Inquiry):

I haven't said enough about the ragged sunits satisfaction in being the one to bind my life...to bring the filthy pieces together,...on its way to more important tasks.

Poetry

• Ode to Anna Moffo and Other Poems (Persea, 1990).
• Rhapsodies of A Repeat Offender (Persea, 1994).
• The Milk of Inquiry (Persea, 1999).
• Model Homes (BOA Editions, 2004).
• Best Selling Jewish Porn Films (Turtle Point, 2006).

Criticism

• Double Talk: The Erotics of Male Literary Collaboration (Routledge, 1989).
• The Queen's Throat: Homosexuality, and the Mystery of Desire (Poseidon, 1993).
• Jackie Under My Skin: Interpreting An Icon (Farrar, Straus, and Giroux, 1995).
• Cleavage: Essays on Sex, Stars, and Aesthetics (Ballantine Books, 2000).
• Andy Warhol (Lipper/Viking, 2001).
• Hotel Theory (Soft Skull Press, 2007).

Fiction

• Moira Orfei in Aigues-Mortes (Soft Skull, 2004).

Opera libretto

• Jackie O