Marek's disease virus (MDV) is a long-recognized oncogenic herpesvirus, which induces lymphoma in its natural host that can be prevented by vaccination. MDV infection provides an excellent biological model for investigating the biology, genetics and immunology of viral oncogenesis. Recently discovered microRNAs (miRNAs) in the MDV genome have been suggested to have regulatory roles during MDV oncogenesis. We have examined the expression profiles of all 22 previously reported miRNAs encoded by MDV-1 in chickens artificially challenged with MDV-GX0101. We found that a subset of the miRNAs was differentially expressed during different phases of the developing disease. These miRNAs show early or late expression during disease progression, accompanied by obvious tissue-specific and differential expression patterns. This temporal and differential tissue distribution suggest that these miRNAs may perform different regulatory roles in switching from latency to lytic replication, immunosuppression, neoplastic transformation or other aspects of lymphoma formation. These reported in vivo expression profiles indicate the potentially functional MDV-1-encoded miRNAs that should be selected for further investigation of their functions in MDV oncogenesis.