Since Sigmund Freud began his revolutionary text Three Essays on the Theory of Sexuality in 1905 with a detailed study of homosexuality, our efforts to understand same-sex attraction and behavior have played a central role in psychoanalytic theory. This paper describes the historical evolution of four psychoanalytic paradigms of male homosexuality – Freud’s search for understanding, homosexuality as illness, homosexuality as health, and the deconstruction of categories of illness and sexuality. A close examination of the underlying assumptions of each paradigm shows the strong influences that cultural context and prejudice have had on psychoanalytic theory and the need for tolerance of uncertainty as a core psychoanalytic value. A clinical illustration of the author’s work with a gay man explores the continuing influence of discredited theories in the minds of patients, and how subsequent theories can be useful in helping patients establish a cohesive and affirmative sexual identity, while also allowing for fluid notions of sexual identity.