The claim that trans women “have female brains” is not supported by the evidence. One of the most persistent problems in this literature is the failure to disentangle “gender identity” from sexual orientation. Several findings interpreted as evidence of a “female-typical” neuroanatomy in trans women closely resemble patterns previously reported in homosexual males. This is precisely why Savic & Arver (2011) restricted their sample to gynephilic trans women (natal males attracted to women), despite the expectation of feminisation, they actually found that major sexually dimorphic neuroanatomical characteristics remained male-typical and explicitly rejected a simple feminisation account. The sexual-orientation confound is particularly important because some of the most widely cited “sex-atypical” findings in trans women are not unique to trans populations. Berglund et al. (2006) reported that homosexual women exhibited hypothalamic responses to putative pheromonal compounds that resembled those observed in heterosexual men, while Savic & Lindström (2005) found that homosexual men displayed female-typical patterns of hypothalamic activation. Similar findings have subsequently been cited as evidence of feminised neurobiology in trans women (Burke et al., 2014), despite the fact that the study cohort were predominantly homosexual relative to natal sex. Any interpretation that attributes these neural characteristics specifically to “gender identity” must therefore explain why comparable effects are observed in homosexual individuals who do not experience gender dysphoria. Cross-sex hormone exposure introduces an equally serious interpretive problem. Estradiol and anti-androgen treatment have been shown to alter cortical thickness, grey matter volume, white matter microstructure, hypothalamic morphology, and patterns of functional connectivity within months of treatment initiation. Hulshoff Pol et al. (2006), for example, observed measurable structural brain changes following hormone treatment, promoting a “sex-atypical” phenotype. Consequently, studies examining participants after years of hormone therapy cannot reliably distinguish pre-existing developmental characteristics from treatment effects. Yet many highly cited papers either include hormonally treated participants or compare treated and untreated individuals in ways that make causal inference difficult. These issues are compounded by small sample sizes, inadequate control for developmental stage, and the fact that male and female brains are not discrete categories but highly overlapping distributions. The most defensible conclusion from the current evidence is that *some* neural features MAY be associated with gender dysphoria, but causality cannot be implied. The much stronger claim that trans women simply “have female brains” remains unproven and is not the consensus finding of contemporary neuroscience.