This study examined the prevalence, course and risk indicators of subthreshold anxiety disorder to determine the necessity and possible risk indicators for interventions. Data were derived from the ‘Netherlands Mental Health Survey and Incidence Study-2’ (NEMESIS-2), a psychiatric epidemiological cohort study among the general population ( n = 4528). This study assessed prevalence, characteristics, and three-year course of subthreshold anxiety disorder ( n = 521) in adults, and compared them to a no anxiety group ( n = 3832) and an anxiety disorder group ( n = 175). Risk indicators for persistent and progressive subthreshold anxiety disorder were also explored, including socio-demographics, vulnerability factors, psychopathology, physical health and functioning. The three-year prevalence of subthreshold anxiety disorder was 11.4%. At three-year follow-up, 57.3% had improved, 29.0% had persistent subthreshold anxiety disorder and 13.8% had progressed to a full-blown anxiety disorder. Prevalence, characteristics and course of subthreshold anxiety disorder were in between both comparison groups. Risk indicators for persistent course partly overlapped with those for progressive course and included vulnerability and psychopathological factors, and diminished functioning. Course analysis were restricted to the development of anxiety disorders, other mental disorders were not assessed. Moreover, due to the naturalistic design of the study the impact of treatment on course cannot be assessed. Subthreshold anxiety disorder is relatively prevalent and at three-year follow-up a substantial part of respondents experienced persistent symptoms or had progressed into an anxiety disorder. Risk indicators like reduced functioning may help to identify these persons for (preventative) treatment and hence reduce functional limitations and disease burden.