A key priority of transgender health research is the evaluation of long-term effects of gender affirmation treatment. Thus, accurate assessment of treatment receipt is critical. The data for this analysis came from an electronic medical records (EMR) based cohort of transgender individuals. A subset of cohort members were also asked to complete a self-administered survey. Information from the EMR was compared with survey responses to assess the extent of agreement regarding transmasculine (TM)/transfeminine (TF) status, hormone therapy receipt, and type of surgery performed. Logistic regression models were used to assess whether participant characteristics were associated with disagreement between data sources. Agreement between EMR and survey-derived information was high regarding TM/TF status (99%) and hormone therapy receipt (97%). Lower agreement was observed for chest reconstruction surgery (72%) and genital reconstruction surgery (84%). Using survey responses as the “gold standard”, both chest and genital reconstruction surgeries had high specificity (95 and 93%, respectively), but the corresponding sensitivities were low (49 and 68%, respectively). A lower proportion of TM had concordant results for chest reconstruction surgery (64% versus 79% for TF) while genital reconstruction surgery concordance was lower among TF (79% versus 89% for TM). For both surgery types, agreement was highest among the youngest participants. Our findings offer assurance that EMR-based data appropriately classify cohort participants with respect to their TM/TF status or hormone therapy receipt. However, current EMR data may not capture the complete history of gender affirmation surgeries. This information is useful in future studies of outcomes related to gender affirming therapy.