Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. These topics are explored in the First Chapter of my dissertation. In the Second Chapter, I explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), I assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. I have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc₁₆₇ cells into G1, S, and G2 subpopulations, I show that even progression through these stages of the cell cycle does not significantly change pairing levels. Applying several strategies in Third Chapter, I use RNAi to identify putative genes important for pairing. Included in these efforts is a novel high-throughput FISH protocol I established to rapidly screen cell cultures for disruptors of pairing. This technique has general applicability for biological questions assayable by FISH. These strategies yielded several putative genes involved in pairing. In the final Fourth Chapter I present data indicating that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing.