Introduction Children with special health care needs (CSHCN) are a high risk population with complex medical issues and needs. It is challenging to care for them in a busy, pediatric practice without understanding how many exist and how best to allocate resources. EMRs can be adapted to develop registries and stratify patients to promote population health management. Methods Adaptations were made to the EMR in September 2013 to capture CSHCN and the associated risk level during well-child visits prospectively. All physicians were trained on the definition of CSHCN and on risk stratification levels 1, 2, 3A and 3B. An analysis using one-way ANOVA for children ages 0–21, seen between September 1, 2011 and August 31, 2015, who were identified and stratified after September 2013, was conducted to determine utilization patterns on hospital admissions, emergency department (ED), subspecialty, and primary care visits. Results A total of 4687 CSHCN were identified during the study period. Of the CSHCN, 45% were Level 1, 41% Level 2, 7% 3A and 7% 3B. There were significant differences in utilization across the tiers of CSHCN with the highest level of stratification (3B) demonstrating the most hospital admissions and primary care visits. Level 3B and level 3A (unstable) had significantly more ED visits. Additionally, as tiers increased from level 1 to 3B there was an increase in subspecialty provider utilization (p
