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During summer enteroviral meningitis is a common cause of febrile illness in children, who are typically hospitalized for 2 to 3 days if bacterial infection is suspected. It has been hypothesized that a sensitive polymerase chain reaction (PCR) assay could quickly confirm the diagnosis and subsequently decrease hospitalization costs. However, to have maximum impact results should be available within 24 h. This necessitates daily assays on small numbers of samples.We examined the clinical utility of a PCR assay during two summers, comparing length of stay and charges. Only during the second summer were results reported to clinicians. Case controls were patients with negative PCR assay results but uncomplicated, presumed viral infections. We determined the cost per case identified with and without pleocytosis as a screen for PCR testing.During the first summer 25% (5/20) of patients with positive PCR assay results remained hospitalized for >2 days. During the second summer 10.2% (6 of 59) of children with positive enteroviral PCR assay results but 37.9% (25 of 66) of case controls remained hospitalized for >2 days. The mean length of hospitalization was significantly (P < 0.05) shorter for patients with positive PCR test results than for case controls. The material cost was ∼$238 per case identified.PCR testing has clinical utility for diagnosis of enteroviral meningitis. Although the demands for daily testing make the test expensive, it appears to be cost-effective with savings related to shorter hospital stays.