Eukaryotic porins or VDACs are a class of transmembrane proteins mainly localized in the outer mitochondrial membrane, whose function is to allow the diffusion of metabolites between the cytosol and the mitochondrion. In Drosophila melanogaster, as in other organisms, a small family of genes encoding porins has been discovered from the sequence of the genome. It is of general interest to understand whether these genes represent functional entities or not, and whether their product is associated to any particular tissue. In previous work we reported about the transcriptional and translational analysis of porin 1 and porin 2, and we proposed the specific presence of the latter in spermatozoa of the fly. In this paper we performed real time RT-PCR quantification of porin 1 and porin 2 transcripts in germ cells of the fly. It indicates that Porin 1 is abundantly expressed in both male and female tissues; Porin 2 instead, is very abundant in testis and it is present in ovaries as well, but in a small amount. The immuno-histological stain of ovaries shows that Porin isoform 1 is selectively targeted to follicular cells while Porin isoform 2 is present in mitochondria of the epithelial sheath cells of the ovariole. The implications of the subcellular distribution of these porin isoforms and the specific localization in germ tissues are discussed.