We previously showed that most VD and DJ gene combinations from newborn surface Ig- pre-B cells had one to three predominant junctions, all of which occurred at the sites of short sequence homologies between the two coding ends. Because the majority of sequences that are present in pre-B cells are in-frame, however, the possibility existed that the frequency of occurrence of predominant IgH junctions was skewed by proliferation of pre-B cells with productive rearrangements. In this study, we analyzed cytoplasmic Ig- pre-B cells, because these cells should not yet be subject to such selection. Two-thirds of the rearrangements from this population in the adult were out-of-frame, suggesting that these rearrangements are unbiased. In newborn cIg- pre-B cells, DJ junctions still showed the same predominant sequences as sIg- pre-B cells, but there was less use of predominant junctions in VD junctions for three of four different VH genes analyzed. For those three VH genes, an average of 30% of the sequences were in-frame. When only the in-frame rearrangements from these cIg- newborn cells were analyzed, frequencies of predominant VD junctions were comparable to those in sIg- pre-B cells. For sequences using the VHS107/V11 gene, however, 67% of the junctions were created at the site of the same dinucleotide in the V gene, and as a result, 73% of the sequences were in-frame. Thus homology-directed recombination does not initially produce as much junctional homogeneity as anticipated in all VD combinations, although it is a frequently used mechanism in the early fetal/neonatal gene rearrangements.