This paper describes an artificial immune system approach (AIS) to modelling time-dependent (dynamic, real time) transportation phenomenon characterized by uncertainty. The basic idea behind this research is to develop the Artificial Immune System, which generates a set of antibodies (decisions, control actions) that altogether can successfully cover a wide range of potential situations. The proposed artificial immune system develops antibodies (the best control strategies) for different antigens (different traffic "scenarios"). This task is performed using some of the optimization or heuristics techniques. Then a set of antibodies is combined to create Artificial Immune System. The developed Artificial Immune transportation systems are able to generalize, adapt, and learn based on new knowledge and new information. Applications of the systems are considered for airline yield management, the stochastic vehicle routing, and real-time traffic control at the isolated intersection. The preliminary research results are very promising.