Introduction The purpose of this research is to investigate autistic traits in youth with gender dysphoria (GD). Earlier research demostrated higher prevalence rates of autism spectrum disorder (ASD) in GD. Method A group of 539 children has registered at the Knowledge and Care center for Gender dysphoria of the VU Medical Centre in Amsterdam. The children went through diagnostic process conform the protocol. During the diagnostic process, the child’s parents completed a standardized questionnaire: the Children’s Social Behavior Questionnaire (CSBQ) for measurement of autistic traits. The experimental group was compared with a healthy control group (N = 232) and a group (N = 554) clinically diagnosed with ASD. Results Significantly more autistic traits were found in youth with GD compared to healthy controls (p = <.05). Youth with GD however, scored significantly lower than youth from the ASD group (p = <.05). Boys with GD and girls with GD did not score significantly different and neither did children and adolescents. Of the participants with GD, 15.4% scored higher than the average of the CSBQ score of the ASD group. Discussion and conclusion Youth with GD showed more autistic traits than youth from the healthy control group. Children with autistic traits could be more susceptible to develop GD because they have more rigid thinking, obsessions and stereotyped behavior. Identity development might be different in children with autistic traits. More research is needed to determine the existence of a possible relation between ASD and GD. Clinicians should be aware of the occurrence of autistic traits in youth with GD because of the problems that this could potentially provide during the diagnostic and treatment process.