In V(D)J recombination, two site-specific cuts are made adjacent to V, D, and J subexons to create four DNA ends, two of which (the coding ends) are joined to generate the exon that encodes the variable domain of the antigen receptor. Although deviations from consensus signal sequences have been reported previously to have a large impact on the efficiency of V(D)J recombination, coding end sequence has been assumed to be neutral with respect to the efficiency of recombination. We have used extrachromosomal V(D)J recombination substrates to undertake a systematic comparison of coding end sequences. Substrates were constructed that contain identical consensus recombination signal sequences, where only the coding ends were varied. Surprisingly, we found that nucleotide sequence at the coding end can affect the efficiency of V(D)J recombination > 250-fold. Variable initiation of recombination appears to account for most of the effect. This finding has mechanistic implications because it indicates that signal-binding proteins involved in V(D)J recombination may have different levels of activity when confronted with coding ends of different sequence. Our results also indicate that coding end sequence must be considered to be among the major factors that shape the antigen receptor repertoire.