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Chromosomally integrated HHV-6 (ciHHV-6) is a rare condition where HHV-6 genome is integrated into human chromosomes and transmitted to the offspring in a Mendelian manner. We report the first case in Greece of ciHHV-6 in an asymptomatic neonate. A full-term male neonate was tested for probable congenital toxoplasmosis due to perinatal maternal serology. While investigation did not reveal anything pathological, film array in CSF turned unexpectedly positive for HHV-6 DNA. PCR in plasma and whole blood were also positive (2,530 cp/ml and 2,200,000 cp/ml respectively) for HHV-6 A and high viral loads persisted despite treatment with ganciclovir. We also performed HHV-6 PCR in neonatal hair follicles with negative results and transcription analysis for the detection of HHV-6 U86, U95 and U90 genes expression in whole blood which turned negative, suggestive of a non-replicating virus, while neonatal serology was indicating vertical transmission. High HHV-6 loads were additionally found in healthy mother and brother. Diagnosis of ciHHV-6 is based on high viral load (> 500,000 cp/ml), in contrast to lower DNA copies found in latent, recurrent or even primary infections. PCR in hair follicles and nails is helpful but not essential. Since ciHHV-6 is not commonly diagnosed especially in immunocompetent paediatric patients, we think that it is important to get familiar with this rare entity, in order to avoid misdiagnosis and unnecessary treatment, while long term follow up might be needed.