Anxiety Disorders (AD) are the most prevalent mental disorders in children and adolescents and a relevant public health problem. The study aimed to determine the prevalence of ADs, the comorbidity, the sociodemographic correlates, and the functional impairment in Spanish school children. The initial sample included 1514 subjects (720 boys; mean age = 10.2), who filled out the Screen for Children’s Anxiety-Related Emotional Disorders (SCARED). In a second phase, 562 subjects at risk and not-at-risk of anxiety were assessed with the Mini-International Neuropsychiatric Interview for Children and Adolescents to obtain DSM-5 diagnoses. Two years later (third phase; mean age 13.5), the SCARED was re-administered. The weighted prevalence of any AD was 11.8%. The most prevalent subtypes were specific phobia (16.2%) and generalized anxiety disorder (GAD) (6.9%). Girls showed higher rates of social anxiety (5.5%) than boys. Apart from being female, low socioeconomic status was also a risk factor for AD. The heterotypic comorbidity of any AD was 40.7%, and the homotypic comorbidity was 35.6%. After controlling for age and other ADs, we found that subjects with GAD had the highest risk of having other depressive disorders and ADs. Only 33.3% of the subjects with any AD had sought professional help. 52.9% of the subjects diagnosed with any of the ADs still had anxiety symptoms after a 2-year follow-up. These findings highlight that in Spain, ADs in early adolescence are an important public health problem and that detection and access to treatment need to be improved.