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Background Many developing countries promote social health insurance as a means to eliminate unmet health needs. However, this strategy may be ineffective if there are barriers to fully utilizing insurance. Methods We analyzed the utilization of social health insurance in 30 hospital districts in the central regions of the Philippines between 2003 and 2007. Data for the study came from the Quality Improvement Demonstration Study (QIDS) and included detailed patient information from exit interviews of children under 5 years of age conducted in seven waves among public hospital districts located in the four central regions of the Philippines. These data were used to estimate and identify predictors of underutilization of insurance benefits - defined as the likelihood of not filing claims despite having legitimate insurance coverage - using logistic regression. Results Multivariate analyses using QIDS data from 2004 to 2007 reveal that underutilization averaged about 15% throughout the study period. Underutilization, however, declined over time. Among insured hospitalized children, increasing length of stay in the hospital and mother's education, were associated with less underutilization. Being in a QIDS intervention site was also associated with less underutilization and partially accounts for the downward trend in underutilization over time. Discussion The surprisingly high level of insurance underutilization by insured patients in the QIDS sites undermines the potentially positive impact of social health insurance on the health of the marginalized. In the Philippines, where the largest burden of health care spending falls on households, underutilization suggests ineffective distribution of public funds, failing to reach a significant proportion of households which are by and large poor. Interventions that improve benefit awareness may combat the problem of underutilization and should be the focus of further research in this area.