The organization of genetic information in eukaryotes is far from straightforward. The interspersion of coding and non-coding regions makes genes up to tens of times larger than they “need” to be if protein coding were the only prerequisite. The presence of untranslated regions in mature mRNAs and the positioning of cis-acting enhancers at considerable distances all contribute to expand the effective size of genes and diminish the apparent informational density of eukaryotic genomes. The relative size of these non-coding elements is quite diverse in distantly related eukaryotes and their distribution does not appear random. Comparing details of gene organization in different groups of organisms provides clues of the possible adaptive significance of some of these differences and may suggest mechanistic explanations to relate a particular type of gene organization to a corresponding functional mode.