Comorbid anxiety disorders are common in children with autism spectrum disorders (ASD). However, studies comparing children with ASD to clinically anxious children are rare. This study investigated anxiety problems and health-related quality of life in children with high-functioning ASD and comorbid anxiety disorders (referred to as the ASD group), compared with children with anxiety disorders (referred to as the AD group). In total, 237 families participated; 115 children were in the ASD group (90 boys and 25 girls, M age = 11.37 years), and 122 children were in the AD group (62 boys and 60 girls, M age = 12.79 years). Anxiety disorders, anxiety symptoms, ASD-like symptoms, and health-related quality of life were assessed with the ADIS-C/P, SCARED-71, CSBQ, and EuroQol-5D, respectively. The number and types of anxiety disorders, as well as their severity, were similar in the ASD and AD groups; however, specific phobias were more common in the ASD group than in the AD group. As compared to the AD group, parents from the ASD group reported their children to have higher scores for total anxiety, social anxiety disorder, and panic disorder. More ASD-like behaviors and higher anxiety severity predicted a lower quality of life, irrespective of group. The results of this study support a highly similar phenotype of anxiety disorders in children with ASD; however, additional research is needed to examine the etiology and treatment effectiveness of anxiety disorders in children with ASD.