INTRODUCTION: Calls for improved measures of gender identity to understand the experience of transgender individuals have grown rapidly in the past 5 years. The need for methodological innovation in this topic area has particular importance for the autistic population since a higher co-occurrence of transgender identities among autistic people has been documented but is not well understood. We use a survey with questions that reflect standards in 2018 to demonstrate how binary conceptualizations of gender did not adequately capture gender identities of transgender autistic individuals. METHODS: Using descriptive statistics from a statewide survey of 1527 autistic adults (mean age 27.5 years), this study compared self-reported survey responses to close-ended standard questions at the time about gender identity to understand shortcomings in capturing this population authentically. RESULTS: We found a mismatch between respondents answering that they were transgender, the sex assigned at birth, and gender identity on separate questions. We postulate that transgender men and women were likely selecting binary responses when asked about gender identity. Furthermore, we found that many qualitative responses reported in the self-selected "other" category reflected nonbinary identities and utilized specific terminology that revealed nuance in how they understood gender identities. CONCLUSIONS: We urge researchers to provide multiple flexible options when measuring gender identity in autistic populations as they are likely to encompass many identities. We endorse best practices for measuring gender identity for autistic research.