Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies. We offer a glimpse into a program which detects TE insertion polymorphisms and discuss practical issues arising from the diversity of TEs and genome architectures. Detecting TE polymorphisms relies on a series of ad hoc criteria because, in contrast to single nucleotide polymorphisms, there is no general way to model TE activity. Signatures of TE polymorphisms in reference-aligned reads depend on the type of TE as well as on the complexity of the genomic background. As a consequence, a basic understanding of the limitations imposed by the data and of what the algorithm is doing is important to obtain reliable results. Here, we hope to convey such a basic understanding and help researchers to avoid some of the common pitfalls of TE polymorphism detection.