This paper provides the first rigorous account of the diverse characteristics of transgender individuals at the population level, using data from Danish population registers. We observe three transgender subpopulations within the same national setting: all who changed thier legal sex (T-Legal, n = 1,995), all who have been assigned trans-related diagnostic codes (T-ICD, n = 1,594), and those who self-identified as transgender in a representative survey (T-Survey, n = 197, weighted n = 44,958). Results show significant differences in the subpopulations’ backgrounds, family, education and labour market characteristics, and healthcare use. These differences extend beyond comparisons with the general population to great variations between each of the transgender subpopulations. Individuals with legal sex changes, and particularly those with trans-related diagnostic codes, face substantial disadvantages across various outcomes. Compared to the general population and the T-Survey subpopulation, the T-Legal subpopulation and the T-ICD subpopulation have significantly higher numbers of psychiatric hospital visits, lower educational attainment, lower annual earnings, and reduced employment rates, also when controlling for background characteristics. Earnings and employment rates remained significantly lower also when controlling for educational attainment. Our results show that the strategy chosen to identify trans individuals in population data has a great impact on the characteristics observed, and that trans individuals captured by surveys do not necessarily represent all transgender individuals, including those who seek to medically or legally transition. Furthermore, our results indicate that high numbers of trans individuals observed in surveys do not necessarily correspond to high demands for gender-affirming treatments or legal sex change. Finally, we show that transgender individuals who seek gender-affirming healthcare constitute a distinct and significantly disadvantaged group, also compared to other trans subpopulations.