In this paper, the maritime fleet renewal problem (MFRP) is extended to include regional limitations in the form of emission control areas. The motivation for including this aspect is that strengthening of emission regulations in such areas is expected to be challenging for deep sea shipping in the years to come. In the proposed model, various means to cope with these stricter emission regulations are evaluated for new vessels, and the possibility of upgrading existing vessels with new emission reduction technology is introduced. We consider future fuel prices to be important for the problem, and have chosen to treat them as uncertain, and thus, a stochastic programming model is chosen. A fleet renewal problem faced by the liner shipping operator Wallenius Wilhelmsen Logistics, concerning whether to use low sulphur fuel or have an exhaust gas scrubber system installed to comply with sulphur regulation in emission control areas from 2015, is used as a case study. Furthermore, tests show that the savings from including the aspect of emission control areas in the MFRP are substantial.