Transcription of the Epstein-Barr virus (EBV) genome in Raji cells superinfected with P3HR-1 EBV in the presence of cycloheximide was compared to transcription in human lymphocytes infected with transforming EBV (B95-8). This was done to identify regions of the EBV genome which contain genes that may mediate initiation of virus replication. Hybridization of 32P-labeled cDNA to cloned fragments of EBV DNA (dot blot hybridization) was employed to identify transcriptionally active regions of the viral genome in these cells. DNA in the BamHI A, F, H, and M restriction fragments was found to encode poly(A) RNA during the early phase of EBV replication. In the absence of cycloheximide the earliest detectable transcripts were transcribed from the BamHI M region. The most transcriptionally active region of the EBV genome in lymphocytes following infection with EBV (B95-8) was the BamHI W-Y-H-F region and, to a lesser extent, the K region. Transcription of the BamHI M region was not detected in these cells. The data suggest that expression of a gene or genes located in the BamHI M region of the EBV genome is an important event in the initiation of EBV replication, whereas expression of the genes in the BamHI W-Y-H-F and K regions may be important in the establishment of latency and cellular immortalization.