Developing improved systems of care for children with special health care needs (CSHCN) requires accurate identification and stratification of this population. This study was designed to assess the ability of a brief screener to identify and stratify CSHCN in a primary care clinic to focus future quality improvement initiatives and allocate resources. All families presenting for health maintenance visits or acute care appointments at an academic primary care clinic between September 5, 2012 and September 28, 2012 were asked to complete the CSHCN Screener.sup.©. This panel of patients was compared to registries previously created by: (1) retrospective chart reviews using published lists of International Statistical Classification of Diseases and Related Health Problems (ICD9) codes for CSHCN and (2) direct physician referral to a clinic case manager providing care coordination services to CSHCN. Screeners identified 246 CSHCN (16.8 % of unique completed screeners). Scores ranged from 0 to 5; higher scores indicate higher levels of complexity. Patients with positive screens had a mean score of 2.4. Patients previously identified by retrospective ICD9 search who completed a screener had a mean score of 1.6 with nearly one-half having negative screens. Patients previously identified by physician referral who completed a screener had a mean score of 2.7 with nearly one-half having scores of 4 or 5. The CSHCN Screener.sup.© can be utilized in an academic primary care clinic to prospectively identify CSHCN and potentially offers a more clinically meaningful method of identification given its inherent ability to stratify this population based on complexity of medical needs.