V, D, and J gene segments rearrange at different frequencies in vivo. In my laboratory, we are interested in determining the reasons for this unequal rearrangement of V genes during B cell development, and also in gaining insights into the mechanisms that control recombination. Every V, D, and J gene segment is flanked on its recombining side(s) by a recombination signal sequence (RSS), which is composed of a conserved heptamer and nonamer, separated by a spacer of conserved length. In this article, we summarize data showing that in many cases the RSS can account for differences in recombination frequencies observed in vivo. The approach that we use is to determine the frequency of initial rearrangement of the V genes in vivo. The RSSs of two V genes are then placed into a competition recombination substrate to determine the relative frequency with which the two RSSs recombine. In one example, we have shown that a single base pair polymorphism in the RSS of a Vkappa gene may play a major role in susceptibility to Haemophilus influenzae type b infection.