CSF-PCR is currently the most sensitive test to diagnose encephalitis due to cytomegalovirus or herpes simplex virus. However, false negative results sometimes arise due to inhibitors in CSF. We have shown that the inhibitory effects may be due to increased levels of proteins and increased cell numbers, but are not due to cellular DNA. Simple techniques were used to remove the inhibitors and successfully apply these methods to CSF specimens that gave equivocal results when tested untreated.