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Human parechovirus (HPeV) and human herpes virus-6 (HHV-6) are acquired commonly in infancy and associated with central nervous system infection. The prevalence of HPeV and HHV-6 in the cerebrospinal fluid (CSF) of infants tested for enterovirus (EV) and herpes-simplex virus (HSV) is unknown. All stored CSF samples from EV or HSV testing in infants less than 6 months of age at Children's Hospital Colorado between January 1, 2010 and December 31, 2011 were tested for HPeV, HHV-6, EV, and HSV by PCR. Clinical characteristics and epidemiological data were collected using retrospective electronic chart review. Of 239 infants tested, 29 cases of EV (12.1%), 7 cases of HPeV (2.9%), 5 cases of HHV-6 (2.1%), and 5 cases of HSV (2.1%) were identified with no bacterial co-infections. HPeV cases occurred between July and October in infants with median age of 24 days. Infants with HPeV had a median maximum temperature of 39 °C, median fever duration of 3 days and median peripheral white blood cell count of 5.2 × 103/μL. HHV-6 cases occurred in infants with median age of 61 days without seasonality. Five percent of infants less than 6 months of age undergoing testing for EV or HSV have HPeV or HHV-6 in the CSF. Targeting testing of HPeV towards febrile infants less than 2 months of age with leukopenia in the late summer to early fall, and HHV-6 towards older infants may increase diagnostic yield. The clinical and fiscal impact of testing infants for HPeV and HHV-6 needs to be determined. J. Med. Virol. 87:829–835, 2015. © 2015 Wiley Periodicals, Inc.