This volume contains the outstanding collection of invited papers and refereed papers selected for the Second International Congress on Mathematical Software, ICMS 2006, held in Castro Urdiales, Spain, September 1-3, 2006. This congress was devoted to all aspects of mathematical software, whose appearance is — in our opinion — one of the most important events in mathematics. Mathematical software systems are used to construct examples, to prove theorems, and to find new mathematical phenomena. Conversely, mathematical research often motivates developments of new algorithms and new systems. Beyond mathematics, mathematical software systems are becoming indispensable tools in many branches of science and technology.