Genetic recombination occurs frequently during replication of picornaviruses. To explore the intracellular site and structures involved in recombination, HeLa cells were infected with poliovirus type 1 Mahoney and type 2 Sabin. The two genomes were located by fluorescent in situ hybridization and confocal microscopy. For hybridization, type-specific fluorescent riboprobes were used to visualize the same genomic region where, in parallel, recombination was demonstrated with type-specific reverse transcription-PCR and sequencing. The hybridization analysis indicated that >85% of the replication complexes contained both type 1 and type 2 RNA sequences aligned at a lateral distance of 50 nm or less. Sequential infection of cells ruled out the possibility that the high percentage of mixed replication complexes was due to aggregation of input virus. Visualization of input genomic RNA over time showed that the viral genomes migrated to relatively few distinct, and thus presumably specific, perinuclear sites where replication started. The first recombinant RNA strands could be detected concomitantly with the onset of RNA replication. The limited number of start sites for replication may be the reason for the observed preferential formation of mixed replication complexes, each accommodating several parental RNA strands and thus allowing recombination.Poliovirus (PV), the prototype member of the family Picornaviridae, represents in many respects the paradigm for research on other plus-strand RNA viruses. Among the fundamental insights gained by PV research is the first discovery of recombination between viral RNA genomes (30, 35). Since then, some light has been thrown on mechanistic aspects of recombination (for a review see references 1 and 57); however, it is not clear in which context of the elaborate structures comprising the viral RNA replication machinery, i.e., the replication complex (4,6,9,12,21,22,51,52), recombination can occur.PV RNA replication is preceded by translation of the incoming viral genome. Translation, initiated at the internal ribosomal entry site (IRES) (42, 43), was reported to be enhanced by binding of the cellular poly(rC) binding protein (PCBP) to the IRES (10,11,25) and, additionally at early stages, by an interaction of eIF4G with the IRES and the poly(A)-bound poly(A) binding protein (PABP) (50). A transition from translation to transcription was thought to be mediated by the newly synthesized viral protein 3CD, which, together with PCBP, binds to the 5Ј cloverleaf of the viral mRNA (23,24,39). Poly(A)-bound PABP then would attach to this complex, leading (again) to a 5Ј-3Ј interaction in the viral plus-strand RNA (29). This interaction was proposed to be a prerequisite for minus-strand RNA synthesis, the first step in genome replication (3,29,53). The second step in viral genome replication is plus-strand RNA synthesis, which proceeds, after multiple initiations, in the partially doublestranded replicative intermediate. The primer for RNA synthesis is VPgpUpU (41), which was found to be ...