By using four methods (histogram, chaos game representation, discrepancy of distance and discrepancy of entropy) at genomic level, the composition of short oligonucleotides and their compositional complexities in three different regions(introns, intergenic DNAs and exons) of genomic DNA from Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster were studied. It can be concluded that: (1) although the genome sizes and gene numbers are quite different, the compositional complexities of exons are similar, while that of noncoding regions are quite different between eukaryotic genomes. From quantitative perspective, this finding means that the degree of organismal complexity is mainly reflected by noncoding regions, but not by exons; (2) in the same regions of genomic DNAs, composition and compositional complexity are highly similar between chromosomes or contigs within eukaryotic genomes; (3) composition differ remarkably little between introns and intergenic DNAs. This suggests that the effects of transcription, splicing, second structure contribute minimally to the constraints operating on these sequences.