This chapter examines the service-oriented architectures (SOA) in conjunction with the enterprise organisational structure integration problem, applied to innovative organization schemes such as virtual enterprises (VE). The evolution of software architectures from traditional to SOA is presented, along with the characteristics, advantages and disadvantages, and problems and difficulties in applying the SOA, while also focusing on the compatibility between SOA and modern organisational structures. The new standard in the service orchestration level, BPEL, is considered as a language for business process modelling, and its impact to the integration problem is examined. New messaging protocols and frameworks such as the enterprise service bus (ESB) or messaging service bus are also examined. The main focus is on the SOA technology trends of modern organisational structures, with regards to their formation and integration. The comparison between SOA and traditional architectures provides a clear path to their adoption in various cases.