Sabin strains of poliovirus used in the manufacture of oral poliovirus vaccine (OPV) are prone to genetic variations that occur during growth in cell cultures and the organisms of vaccine recipients. Such derivative viruses often have increased neurovirulence and transmissibility, and in some cases they can reestablish chains of transmission in human populations. Monitoring for vaccine-derived polioviruses is an important part of the worldwide campaign to eradicate poliomyelitis. Analysis of vaccine-derived polioviruses requires, as a first step, their isolation in cell cultures, which takes significant time and may yield viral stocks that are not fully representative of the strains present in the original sample. Here we demonstrate that full-length viral cDNA can be PCR amplified directly from stool samples and immediately subjected to genomic analysis by oligonucleotide microarray hybridization and nucleotide sequencing. Most fecal samples from healthy children who received OPV were found to contain variants of Sabin vaccine viruses. Sequence changes in the 5 untranslated region were common, as were changes in the VP1-coding region, including changes in a major antigenic site. Analysis of stool samples taken from cases of acute flaccid paralysis revealed the presence of mixtures of recombinant polioviruses, in addition to the emergence of new sequence variants. Avoiding the need for cell culture isolation dramatically shortened the time needed for identification and analysis of vaccine-derived polioviruses and could be useful for preliminary screening of clinical samples. The amplified full-length viral cDNA can be archived and used to recover live virus for further virological studies.Live trivalent oral poliovirus vaccine (OPV) prepared from attenuated Sabin strains is highly efficacious, and its worldwide use resulted in eradication of poliomyelitis in the United States (41) and most other countries (37,38). Roughly half of the approximately eight cases reported yearly in the United States involved immunodeficient individuals. Vaccine-derived poliovirus (VDPV) strains isolated from stools of individuals with vaccine-associated paralytic poliomyelitis (VAPP) have been found to contain a number of mutations and exhibit increased neurovirulence. While some of the mutations occurring in VDPV strains restore the sequences present in the wild-type progenitors of the vaccine strains (direct reversions), other mutations either are incidental or are second-site suppressors of attenuated phenotype. All three Sabin strains contain a single base change in the same domain of the 5Ј untranslated region (5Ј-UTR) that contributes to the attenuated phenotype, as indicated by increased neurovirulence in strains where this base change is reversed or altered by a compensating mutation (17, 31). Such Sabin strain variants with reversion in the 5Ј-UTR have been identified in type 3 (5, 17), type 2 (30), and type 1 (9, 24) isolates from patients with VAPP, as well as from healthy vaccine recipients (1,11,16,42). Isolation of suc...