Neonatal jaundice is one of the most common problems leading to prolonged hospitalization of the newborn. Therefore, an effective low-risk, low-cost therapy reducing hospitalization is highly desirable. Plain dried agar, an extract of seaweed, is low cost and low risk; it can bind bilirubin in the gut, decreasing its enterohepatic circulation, thereby decreasing serum levels. Because of conflicting conclusions in the studies of agar's effectiveness in the prevention and treatment of neonatal jaundice, a meta-analysis of their methodologies was done. Criteria for assessing prospective controlled therapeutic trials of agar were established in six areas: hypothesis and clinical outcome, patient selection, treatment group allocation, therapeutic maneuver, use of cotherapies, and data analysis. Nine prospective clinical trials of agar therapy were evaluated using these six criteria. The seven studies with negative conclusions regarding agar's efficacy failed to meet the criteria in several categories: patient selection, therapeutic maneuver, use of cotherapies, or data analysis. All of the studies, including the positive studies, were at risk for biased treatment allocation. Although the pooled data analysis suggests that prophylactic agar treatment is associated with reduced peak serum bilirubin levels, this observation must be interpreted cautiously in light of heterogenous patient populations and the methodologic problems described. Based on this meta-analysis, agar therapy for neonatal jaundice can neither be recommended nor rejected. The methodologic analysis gives clear guidance for future research concerning the effectiveness of agar in treating neonatal jaundice and provides a model for meta-analysis of other prospective trials in pediatrics.