Human herpesvirus 6 (HHV-6), which is present in more than 90% of the human, is known to cause infectious diseases in immuno-compromised patients, e.g., transplant patients. To clarify the possible role of the pattern of expression of HHV-6 genes in various types of HHV-6B infection, we sought to determine whether or not viral DNA microarray could be used for detailed characterization of viral transcription using a HHV-6B DNA microarray that contains 97 known open reading frames of HHV-6B. A subset of genes are preferentially expressed in persistent infection: U16 (IE-B, transactivator, US22 gene family), U18 (IE-B, homolog to HCMV IE glycoprotein), U20 (glycoprotein), U27 (DNA polymerase processivity transactivator), U82 (gL, gH accessory protein), U83 (chemokine), U85 (OX-2 homology, glycoprotein), U90 (IE-A), and U94 (transactivator), respectively. Although the function of each HHV-6B is not fully understood, our study suggests that comprehensive analysis of HHV-6B transcription is useful not only to clarify the pathogenesis of the virus but also to develop new strategies for anti-viral drugs.