Kaposi's sarcoma (KS) is the signature pathology of AIDS. KS-associated herpesvirus (KSHV/HHV-8) is causally linked to KS. Here, we report the first complete profile of KSHV transcription in primary KS lesions using a novel, real-time PCR array. The KSHV latency I mRNAs [latency-associated nuclear antigen (LANA)/orf73, v-cyclin/orf72, and v-FLIP/orf71] were invariably present in all biopsies. Yet, viral lytic mRNAs were detectable in only a subset of tumors. Interestingly, there was a difference in the expression pattern of the viral IFN-regulatory factors (vIRFs) encoded by KSHV. The vIRF-1/K9 clustered with LANA in KS, in contrast to its homologue, vIRF-3/LANA-2, which is transcribed only in KSHV-associated lymphomas. This suggests that the various vIRFs encoded by KSHV are important for KSHV latency as well as KS tumorigenesis and that their redundancy may be explained in part by a tissue-specific regulation. Clinical KSHV transcriptional profiling as described here will prove useful for the identification of KS tumor markers for diagnosis and as potential drug targets. Stratification by KSHV lytic transcription can identify lesions with a high percentage of lytically infected cells, which may respond to antiviral drugs.