This study examined the experiences that lesbian, gay, bisexual, transgender, queer, questioning, and two-spirit (LGBTQ2S) homeless youth have in shelters and the disjunctures that occur for this population in Toronto’s shelter system. The attitudes and behaviors of shelter workers and management toward LGBTQ2S youth were also explored. A critical action research approach, informed by critical ethnography and institutional ethnography was employed. Thirty-three people participated in this study in the Greater Toronto Area. The study triangulated data from interviews, focus groups, observations, and document analysis. The systemic enactment of homophobia, transphobia, and hegemonic masculinity are often normalized in shelters and create significant barriers to safe,accessible, and supportive services for LGBTQ2S youth. Excessive bureaucratic regulation and the lack of necessary bureaucratic regulation in highly significant areas play a key role in creating the disjunctures that occur for LGBTQ2S youth in shelters.