A total of 525 cerebrospinal fluid (CSF) samples submitted during the 2007 and 2008 enteroviral seasons were included in a study to determine the prevalence of and potential risk factors for invalid Cepheid GeneXpert enterovirus assay (GXEA) results, as well as possible solutions for the problem. The invalid GXEA results were reported for 43 (8.2%) specimens and correlated with increased visibility of red blood cells (P < 0.0001) but not with CSF xanthochromia and clotting. Invalid GXEA result rates were markedly diminished by 82.1% and 96.0% and test sensitivities were minimally decreased by 1.7% and 3.6% when these specimens were tested at a 1:5 dilution and after a freeze-thaw cycle, respectively.Enterovirus (EnV) meningitis can be difficult to distinguish from disease caused by other etiologic agents when patients present with nonspecific pathogenic symptoms and signs, such as fever, headache and stiff neck, and pleocytosis in cerebrospinal fluid (CSF) (4,8,9). Nucleic acid amplification-based procedures for the detection of EnV RNA in CSF have replaced cell culture as the test of choice (10,11,14). The GeneXpert enterovirus assay (GXEA; Cepheid, Sunnyvale, CA) is designed as an integrated system combining specimen processing, EnV amplification, and detection in a disposable cartridge which takes 2.5 h to detect EnV from CSF (6,7,12). It is designed for on-demand testing, such that "stat" PCR results can be returned to the emergency room physicians in time for patient management decisions to be made in real time. The system includes an internal control that provides a means to detect amplification inhibitors. When the internal control does not amplify, the presence of an amplification inhibitor is assumed and the result is reported as "invalid." Invalid results, if and when they occur, could delay patient management in the emergency setting.We performed a 2-year prospective study to determine the prevalence of invalid GXEA results and explore the potential risk factors related to the occurrence of invalid results. We also validated two alternative procedures to minimize the occurrence of these invalid results for EnV detection in CSF.(This study was presented in part at the 25th Annual Meeting of the Pan American Society for Clinical Virology, Daytona Beach, FL, 19 to 22 April, 2009.) Clinical samples. CSF specimens submitted to Vanderbilt University Medical Center between 1 April 2007 and 20 September 2008 for detection of EnV by PCR were collected consecutively. Specimens with enough leftover volume and still unfrozen after the completion of diagnostic testing were included in the study.Determination of CSF characteristics. Each CSF sample was visually examined for visible red blood cells (RBCs), clotting, and the presence of xanthochromia. RBC visibility was graded semiquantatively on a scale using rankings of clear, 1ϩ, 2ϩ, 3ϩ, and 4ϩ. These grades were based on specimen colors and turbidities which roughly correspond to CSF RBC counts of Ͻ200/l (clear), 200 to 5,000/l (1ϩ), 5,000 to 75,000/l (2ϩ), 75...