In the last few years association and linkage disequilibrium studies have come to play an important role in the search for the location of genes underlying certain traits, since linkage analyses provide less accurate estimations of the positions of the genes as the complexity and rareness of the traits increase, partly due to the difficulty of getting large and informative enough samples. These approaches have been proven to be able to narrow the distance between the expected site of the locus and the nearest marker, and to reduce sample requirements in terms of size and structure when compared to those needed for linkage studies to obtain evidence for a genes involvement. On the other hand, the lack of robustness with respect to population history and structure makes them still a subject of constant research. The kind of sample, the analysis to perform, the approach of seeking association with a particular marker versus conducting a complete scan of a wide part of the genome, the type and number o f markers used, the nature of the trait (discrete or continuous), and the underlying model of the disequilibrium are some of the different factors needed to be taken into account when considering association studies. Any of them would by itself justify an individual review, but it is our intention to provide an overall perspective of the different approaches available at the current time.