In this paper the fairness of some methods of allocating seats in a proportional representation (PR) voting system is investigated. Different PR systems are in use throughout the democratic world, but the primary focus here is the method used in South Africa, namely the largest remainder method with a Droop quota. It is shown that as the number of parties increases, the number of lost votes (votes not used to allocate seats) increases when using this method. Other existing allocation methods are discussed and compared with each other as well as with three optimisation methods (based on mathematical programming) introduced in this paper. Applying these mathematical programming methods results in allocations that are more fair than the existing methods of seat allocation, if South African voting data are used. These mathematical models attempt to minimise a number of different measures of the deviation between the actual percentage of votes received and the percentage of seats allocated to a certain party. Ideally this deviation should be zero, but due to the discrete nature of seats this is virtually impossible to achieve.