Nonserotypeable isolates predominate in epidemic conjunctivitis caused by Streptococcus pneumoniae. Previous evaluations of outbreaks of pneumococcal conjunctivitis have relied on epidemiologic factors and the nontypeability of the isolates to infer that a single clone was involved. In the present study, BOX-polymerase chain reaction DNA analysis was used to characterize nonserotypeable S. pneumoniae isolated by conjunctival culture during a recent conjunctivitis outbreak and to compare these isolates with those from outbreaks described earlier. The recent outbreak was caused by a single pneumococcal clone. Outbreaks in separate parts of the United States in 1980-1981 were all caused by the same clone. Cluster analysis revealed a high degree of genetic relatedness among isolates causing conjunctivitis compared with that among other nonserotypeable S. pneumoniae, with the closest relatedness being found among the 1996 and 1980-1981 conjunctival isolates.