The purpose of this study was to determine whether immunization of children during treatment in an Emergency Department (ED) affects subsequent compliance with primary care. This cohort study of children immunized in the ED and matched controls was conducted in the ED and the pediatric clinic in an urban, tertiary care, pediatric hospital. Forty children were enrolled in study and control groups. There were no differences in age, race, sex, insurance status, temperature on arrival, and discharge diagnoses between groups. The immunization status by parental report and as documented in the clinic records was similar for immunized and control patients. There was no difference in attendance at health maintenance visits during the six months after the ED visit between immunized and control patients. No differences in receipt of immunizations or in immunization status were noted after six months. The sample size has adequate power to conclude that the difference in subsequent compliance with primary care between immunized and control patients is less than 50%. Parents reported their child's immunization status incorrectly in 23% of cases. Patients receiving measles immunization in the ED had already been immunized in 18% of cases. Unnecessary subsequent immunization of study patients occurred in 28% of cases. In conclusion, immunization in an ED does not have a large effect on subsequent compliance with primary care. In the ED, parents are an unreliable source of information about immunization status. An immunization database could reduce the frequency of inappropriate immunization.