Primary spermatocyte nuclei of Drosophila melanogaster contain three prominent lampbrush-like loops. The development of these structures has been associated with the transcription of three fertility factors located on the Y chromosome, named kl-5, kl-3 and ks-1. These loci have huge physical dimensions and contain extremely long introns. In addition, kl-3 and kl-5 were shown to encode two putative dynein subunits required for the correct assembly of the sperm axoneme. Here, we show that both the kl-5 and kl-3 loops are intensely decorated by monoclonal antibodies recognizing triple-stranded nucleic acids, and that each loop presents a peculiar molecular organization of triplex structures. Moreover, immunostaining of Drosophila hydei primary spermatocytes revealed that also in this species -which diverged from D. melanogaster 58 million years ago -Y-loops are decorated by anti-triplex antibodies, strongly suggesting a conserved role of loop-associated triplexes. Finally, we showed that in D. melanogaster wild-type lines that are raised at the non-permissive temperature of 31±0.5°C (which is known to induce male sterility in flies) both the triplex immunostaining and the axonemal dynein heavy chains encoded by kl-3 and kl-5 are no longer detectable, which suggests a functional correlation between loop-associated triplexes, the presence of axonemal proteins and male fertility in fly. Journal of Cell Science 1606 triplexes, the most stable triads are those involving a protonated cytosine (C + ) formed by C + *GC triad and T*AT nucleotides (the asterisks mark the nucleotides on the third strand). Notably, these sequences are overrepresented in all eukaryotic genomes (Behe, 1987; Behe, 1995), as well as in eukaryotic viruses (Beasty and Behe, 1988). It is also possible to have triplex formation without homopurine stretches, and these triplexes seem to be as stable as the others at least under certain conditions (Dayn et al., 1992). Although triplexes are well characterized in vitro, their biological significance in living organisms is still under discussion (Zain and Sun, 2003). It has been demonstrated that, upon formation, these structures can frequently downregulate (Cooney et al., 1988; Birg et al., 1990; Faria et al., 2000;Faria et al., 2001) and sometimes upregulate (reviewed in Faria and Giovannangeli, 2001) gene expression, a fact which demonstrates their potential in gene control and suggests their use in gene therapy (Wang et al., 1995;Vasquez et al., 2000) (for a review, see Rogers et al., 2005). The structures are also able to impair DNA polymerization (Dayn et al., 1992), and can influence DNA recombination and repair (Faruqi et al., 1996;Wang et al., 1996;Faruqi et al., 2000;Vasquez et al., 2002;Kalish et al., 2005;Raghavan et al., 2005) (for reviews, see Seidman and Glazer, 2003; Chin et al., 2007). Triplexes might also have a role in chromatin organization of both interphase nuclei (Agazie et al., 1996;Ohno et al., 2002) and mitotic chromosomes . Recently, it has been demonstrated that a triplestran...