We recruited a cohort of 157 recent orphans and 480 non-orphans aged 9–15 in a region of high HIV/AIDS mortality in South Africa using stratified cluster sampling to determine the impact of recent parental death on health and food insecurity of school- going orphans compared to non-orphans over time. Between September 2004 and June 2007, household heads, caregivers, and children were interviewed at three annual inter- vals. Bivariate associations and multivariate models were assessed using generalized estimating equations (GEE). In the health domain, compared to non-orphans, double orphans were more likely to report worse health status and being very ill in the previous 12 months. For those who reported being very ill, maternal or paternal orphans were more than twice as likely not to seek care than non-orphans; no differences were found for double orphans. For nutrition and food insecurity, maternal or paternal orphans were more likely not to have eaten dinner and to have gone to bed hungry the previous night compared to non-orphans; no differences were found for double orphans. Overall, recent school-aged orphans were disadvantaged in health and food insecurity within two years after the death of a parent, compared to their non-orphaned counterparts, but the disparities were smaller than expected. No changes in health, nutritional status, or food insecurity were apparent over the three study rounds. Longer term effects into adulthood may well be more pronounced and warrant careful longitudinal investigation.