Polyploidy is an important evolutionary mechanism in plants that can lead to novel genetic and phenotypic variation, conferring heterosis or the ability to exploit new environmental niches and undergo speciation. In order to observe the early events following polyploidy formation, fifty resynthesized lines of Brassica napus derived from doubled haploid homozygous diploid parents of Brassica oleracea and Brassica rapa were created and selfed to the S5 generation. The lines were compared to the parents and assayed for changes in genome structure, gene expression, and phenotype at both the S0 and S5 level using a combination of RFLPs, SSRs, cDNA-AFLPs, and RT-PCR SSCP. Genome structure and gene expression appeared quiescent and additive immediately following polyploidization and phenotypic variability was low. However, by the S5 generation numerous and variable genome changes, non-additive patterns of gene expression, and phenotypic divergence was identified among the lines. Estimated mapping locations of observed genome changes were obtained using maps of the parental chromosomes. In support of previous data, structural genome changes, including DNA loss and chromosomal rearrangements, may be an important source of de novo variation in newly resynthesized Brassica polyploids. In addition, the location of chromosomal rearrangements in these resynthesized Brassica allopolyploids is in agreement with studies that have found non-reciprocal transpositions in natural genotypes of Brassica napus, suggesting that certain regions of this allopolyploid genome are more likely to undergo structural changes as seen in Helianthus hybrids. Various mechanisms such as translocations, transpositions, and gene conversion will be discussed in light of these results and in comparison to rapid genomic changes seen in resynthesized allopolyploid wheat.