To look for evidence of intrafamilial infection, we isolated 107 Helicobacter pylori clones from biopsied specimens taken from both parents and four children. We compared the sequences of two housekeeping genes (hspA and glmM) from these clones with those of 131 unrelated strains from patients living in different geographic regions. Strain relationships within the family were determined by analyzing allelic variation at both loci and building phylogenetic trees and by using multilocus sequence typing. Both hspA- and glmM-based phylogenetic trees showed East Asian and African branches. All samples from family members showed natural mixed infection. Identical alleles found in some strains isolated from the children and parents, but not in the strains isolated from unrelated patients, demonstrated that strains have circulated within the family. Several mechanisms, such as point mutations, intragenic recombination, and introduction of foreign (African) alleles, were shown to enhance strain diversity within the family.