Universal periodic high-dose vitamin A capsule distribution is a cost-effective intervention to increase child survival in developing countries. It is unclear whether children who are missed by the program are at higher risk for malnutrition and infectious disease morbidity. Based on data from the Nutritional Surveillance System, we compared nutritional status and other health indicators of children aged 12-59 mo in rural Indonesia who did and did not receive a vitamin A capsule within the last 6 mo. A total of 241,087 of 335,034 children (72.0%) received a vitamin A capsule between 1999 and 2003. In children who did and did not receive a vitamin A capsule, respectively, the proportion with weight-for-age, height-for-age, and weight-for-height Z scores <-2 were 37.0 vs. 42.5%, 39.2 vs. 45.6%, and 6.9 vs. 7.4% (P < 0.0001). Similarly, the proportion with anemia, diarrhea during the last wk, current diarrhea, and current fever was 49.2 vs. 54.8%, 6.7 vs. 8.4%, 4.4 vs. 6.0%, and 1.4 vs. 1.7% (P < 0.0001). Children who did not receive vitamin A were also less likely to have received childhood immunizations and belonged to families with higher infant and under-5-y child mortality than children who receive vitamin A. Although a lack of access to other public health interventions and demographic factors may also contribute to the rate of malnutrition in children missed by the vitamin A capsule program, it is likely that increased coverage of vitamin A supplementation would help to maximize the benefits for child survival.