Gender nonconformity refers to the extent to which a person’s gender identity, gender role and/or gender expression differs from the cultural norms prescribed for people of a particular sex, within a certain society and era. Most data on gender nonconformity focus on the prevalence of gender dysphoria (which also includes a distress factor) or on the number of legal sex changes. However, not every gender nonconforming individual experiences distress or applies for treatment. Population-based research on the broad spectrum of gender nonconformity is scarce and more information on the variance outside the gender binary is needed. This study aimed to examine the prevalence of gender incongruence (identifying stronger with the other sex than with the sex assigned at birth) and gender ambivalence (identifying equally with the other sex as with the sex assigned at birth) based on two population-based surveys, one of 1,832 Flemish persons and one of 2,472 sexual minority individuals in Flanders. In the general population, gender ambivalence was present in 2.2% of male and 1.9% of female participants, whereas gender incongruence was found in 0.7% of men and 0.6% of women. In sexual minority individuals, the prevalence of gender ambivalence and gender incongruence was 1.8% and 0.9% in men and 4.1% and 2.1% in women, respectively. With a current Flemish population of about 6 million, our results indicate a total of between 17,150 and 17,665 gender incongruent men and between 14,473 and 15,221 gender incongruent women in Flanders.