The RAG1 and RAG2 proteins initiate V(D)J recombination by making specific double-strand DNA breaks at recombination signal sequences. We show here that RAG1 and RAG2 bind specifically to this sequence, forming a stable protein-DNA complex. The complex requires the conserved heptamer and nonamer motifs of the recombination signal as well as both the RAG1 and RAG2 proteins. This complex is able to either nick or form hairpins at the V(D)J signal sequence, depending on the divalent cation present. A complex trapped using Ca2+ is subsequently active when transferred to Mg2+ or Mn2+. After cleavage, the complex is destabilized and the RAG proteins dissociate. We term this early precursor in the V(D)J recombination reaction a "stable cleavage complex."