We study the correlation between introns and modules, compact regions of protein structure, in genes whose products have a known 3-dimensional structre and which are homologous between bacteria and eukaryotes. Using two definitions of modules, we show that phase zero introns, those that lie between the codons, are significantly correlated with the boundaries of modules while introns that lie in phases one and two, that interrupt the codons are not so correlated. Furthermore, intron positions that are philogenetically ancient, matching between two kingdomes, are more correlated with module boundaries than are other positions. We will discuss the significance of these findings, which suggest that some of the phase zero introns are residues of the original construction of the genes while the phase one and two introns may have been added later in evolution.