The purpose of the presented work has been to give a short summary of the origins of many uncertainties arising in the designing and performance assessment of a repository for spent nuclear fuel. Some different methods to treat these uncertainties is also included. The methods and conclusions are in many cases general in the sense that they are applicable to many other disciplines where simulations are used. As a conclusion it may be noted that uncertainties of different origin have been discussed and debated, but one large group, e.g. computer simulations, where the methods to make a more explicit investigation exists, have not been investigated in a satisfying way. 50 refs.