Association studies using SNPs provides one of the best tools that we have at the moment for looking for genes involved in physical traits. However the studies should be carefully designed from the very beginning in all the steps of the procedure: pre-genotyping, genotyping and the mathematical analysis of the results. If the actual knowledge is correctly applied in the design of the study the probability of being successful in finding an association can be considerably increased. Improved statistical analysis techniques are helping in the robustness of the findings. The current consensus from the literature indicates that this would be a good time to investigate complex or quantitative traits via dense SNP genotyping, and a number of studies have been published, providing potential models. The state of the art of candidate genes for pigmentation, stature and facial morphology is described.