The structure and integration patterns of equine infectious anemia virus (EIAV) proviral DNA and the patterns of viral transcription were examined in persistent and cytopathic infections of cultured cells. The results of Southern blot analyses indicated that, in persistently infected cells, about 30% of the EIAV provirus exists as randomly integrated DNA, while the remaining 70% is equally divided between unintegrated linear and closed circular forms. The cytopathic infection, in contrast, is characterized by levels of integrated provirus ranging from 65 to more than 90% of the total proviral DNA, depending on the extent of cytopathology exhibited by the virus strain employed. In both persistent and cytopathic infections, extensive Northern (RNA) blot analyses have revealed the presence of two major virus-specific transcripts, an 8.2-kilobase (kb) full-length genomic mRNA and a 3.5-kb single-spliced mRNA. A low-abundance 1.5-kb mRNA, presumably formed by a double-splicing event of the full-length RNA, was also detected in the cytopathic EIAV infection. The two major viral transcripts are present in approximately equal quantities in persistently infected cells, while the cytopathic infection reveals nearly a 30-fold higher level of viral transcripts in which the 3.5-kb species constitutes over 75% of the total viral mRNA. The relatively high proportion of proviral DNA integration and the simple pattern of viral transcription observed during EIAV infections appeared to be different from the generally observed patterns of predominantly unintegrated proviral DNA and multi-spliced viral mRNAs in cells infected with other lentiviruses such as visna virus or human immunodeficiency virus type 1. Moreover, the data suggested that the cytopathology of EIAV may be correlated in part with the degree of proviral DNA integration and levels of viral mRNA in infected cells, particularly that of the spliced 3.5-kb mRNA.