Abstract Introduction Gender dysphoria (GD) is characterized by a marked incongruence between experienced gender and one's gender assigned at birth. Transsexual individuals present a higher prevalence of psychiatric disorders when compared to non-transsexual populations, and it has been proposed that minority stress, i.e., discrimination or prejudice, has a relevant impact on these outcomes. Transsexuals also show increased chances of having experienced maltreatment during childhood. Interleukin (IL)-1β, IL-6, IL-10 and tumor necrosis factor-alpha (TNF-α) are inflammatory cytokines that regulate our immune system. Imbalanced levels in such cytokines are linked to history of childhood maltreatment and psychiatric disorders. We compared differences in IL-1β, IL-6, IL-10 and TNF-α levels and exposure to traumatic events in childhood and adulthood in individuals with and without GD (DSM-5). Methods Cross-sectional controlled study comparing 34 transsexual women and 31 non-transsexual men. They underwent a thorough structured interview, assessing sociodemographic information, mood and anxiety symptoms, childhood maltreatment, explicit discrimination and suicidal ideation. Inflammatory cytokine levels (IL-1β, IL-6, IL-10 and TNF-α) were measured by multiplex immunoassay. Results Individuals with GD experienced more discrimination (p = 0.002) and childhood maltreatment (p = 0.046) than non-transsexual men. Higher suicidal ideation (p < 0.001) and previous suicide attempt (p = 0.001) rates were observed in transsexual women. However, no differences were observed in the levels of any cytokine. Conclusions These results suggest that transsexual women are more exposed to stressful events from childhood to adulthood than non-transsexual men and that GD per se does not play a role in inflammatory markers.