Four natural variants of satellite tobacco mosaic virus (STMV) were compared with each other and with the type strain. Differences were detected in double-stranded RNA, single-stranded RNA, and virion electrophoretic mobility patterns, while the size and antigenicity of the coat protein were similar for all. RNase protection assays detected differences in the genomes of each of the four new variants, which differed not only from each other, but also from that of type STMV. Infectious RNA transcripts were made from complementary DNA clones of one variant (STMV 10) with a genome apparently smaller than that of type STMV. A 71-base deletion in the region that contains the 6.8-kDa protein in type STMV was detected by sequence analysis of the STMV 10 clones, a result that is confirmed by the lack of a 6.8-kDa in vitro translation product for STMV 10. Only minor sequence differences exist elsewhere in the genome compared with that of type STMV. Type STMV and STMV 10 each successfully cross-protected against the other when tobacco plants were inoculated 10 days apart.