Transposable elements (TEs) are mobile DNA sequences that are a source of mutations and can target specific sites in host genome. Understanding the molecular mechanisms of TE target site preferences is a fundamental challenge in functional and evolutionary genomics. Here we used accurately mapped TE insertions in the Drosophila melanogaster genome, from large-scale gene disruption and resequencing projects, to better understand TE insertion site mechanisms. First we test predictions of the palindromic target site model for DNA transposon insertion using artificially generated P-element insertions. We provide evidence that the P-element targets a 14 bp palindromic motif that can be identified at the primary sequence level that differs significantly from random base composition in the D. melanogaster genome. This sequence also predicts local spacing, hotspots and strand orientation of P-element insertions. Next, we combine artificial P-element insertions with data from genome- wide studies on sequence properties of promoter regions, in an attempt to decode the genomic factors associated with P-element promoter targeting. Our results indicate that the P-element insertions are affected by nucleosome positioning and the presence of chromatin marks made by the Polycomb and trithorax protein groups. We provide the first genome-wide study which shows that core promoter architecture and chromatin structure impact P-element target preferences shedding light on the nuclear processes that influence its pattern of TE insertions across the D. melanogaster genome. In an effort to understand the natural insertion preferences of a wide range of TEs, we then used genome resequencing data to identify insertions sites not present in the reference strain. We found that both Illumina and 454 sequencing platforms showed consistent results in terms of target site duplication (TSD) and target site motif (TSM) discovery. We found that TSMs typically extend the TSD and are palindromic for both DNA and LTR elements with a variable center that depends on the length of the TSD. Additionally, we found that TEs from the same subclass present similar TSDs and TSMs. Finally, by correlating results on P-element insertion sites from natural strains with gene disruption experiments, we show that there is an overlap in target site preferences between artificial and natural insertion events and that P-element targeting of promoter regions of genes is a natural characteristic of this element that is influenced by the same features has the artificially generated insertions. Together, the results presented in this thesis provide important new findings about the target preferences of TEs in one of the best-studied and most important model organisms, and provide a platform for understanding target site preferences of TEs in other species using genomic data.