This paper introduces a new methodology based on risk analysis for the selection of the best route for the transport of a hazardous substance. In order to perform this optimisation, the network is considered as a graph composed by nodes and arcs; each arc is assigned a cost per unit vehicle travelling on it and a vehicle capacity. After short discussion about risk measures suitable for linear risk sources, the arc capacities are introduced by comparison between the societal and individual risk measures of each arc with hazardous materials transportation risk criteria; then arc costs are defined in order to take into account both transportation out-of-pocket expenses and risk-related costs. The optimisation problem can thus be formulated as a 'minimum cost flow problem', which consists of determining for a specific hazardous substance the cheapest flow distribution, honouring the arc capacities, from the origin nodes to the destination nodes. The main features of the optimisation procedure, implemented on the computer code OPTIPATH, are presented. Test results about shipments of ammonia are discussed and finally further research developments are proposed.