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Physical vestigial traits, such as wisdom teeth, are human structures that no longer serve the adaptive purpose they once did in our evolutionary past. When they erupt and become inflamed in modern society, they are typically identified as such, diagnosed and treated. Science has afforded much less attention to vestigial psychosocial or behavioral traits (emerging from neural remnants of our ancient past). There was even a lessening of Freud’s emphasis on the evolutionary nature of psychopathology early on in the post-Freudian era of psychoanalysis. This paper proposes that we investigate homophobia as a psychosocial vestigial trait that is maladaptive in contemporary society – psychopathology deserving of potential classification as such, with different subtypes, comorbidities and relevant interventions. Homosexuality was classified as psychopathology in the first edition of the Diagnostic and Statistical Manual (DSM) in 1952—without any empirical evidence to justify its inclusion as a mental illness. Although the diagnosis was partially removed in 1973, no steps were taken to “scientifically exonerate” or to mitigate the decades of damage done by this labeling. Some fundamentalist religious ideologies and their doctrines continue to identify homosexuality as a malady and abomination. This paper proposes that this type of indoctrination infects and inflames vestigial neural structures that have been conserved from our evolutionary past. We need our “scientific bible” to counter these beliefs and to identify and research the pathology of homophobia. Science challenges harmful religious beliefs and politically motivated ideologies that have found their way into a culture’s imagination. Homophobia deserves to be viewed through a macroscopic lens as a maladaptive vestigial trait in contemporary society. Our primitive ancestors had to discriminate against those they perceived as different from their clan to enhance their survival. It was adaptive back then; it is maladaptive today. Homophobia, along with other forms of discrimination against differences, must be investigated and highlighted as psychopathological.