In less than 10 years after the implementation of the World Anti-Doping Code and of the International Standard for Laboratories and its related Technical Documents, the analysis of human samples for the purpose of anti-doping testing has undergone a noticeable evolution. The research programs developed by the anti-doping organizations, and in particular the World Anti-Doping Agency (WADA), have created an unprecedented momentum in anti-doping science to strengthen the existing analytical methods, as well as to support the development and implementation of new and more sophisticated methodologies by the WADA-accredited laboratories. The integration of technical novelties into the analytical menus has been stimulated by the never-ending challenges posed by the adoption of more complex doping regimens by some athletes and their entourage. This increased sophistication of doping practices has also been reflected in the addition of new doping substances or methods on the WADA Prohibited Substances and Methods List. The integration of new anti-doping scientific paradigms with the development of the Athlete Biological Passport or the foreseen implementation of genomic- and proteomic-based tests constantly reshapes the environment of anti-doping analysis. This article provides a multiangle perspective on some of the key analytical challenges that anti-doping analytical science will face in 2012 and beyond.