Satellite links are expected to be one important component of the next-generation Internet. New satellite system architectures are being envisaged to be fully IP based and support digital video broadcasting and return channel protocols (e.g. DVB-S, DVB-S2 and DVB-RCS). To make the upcoming satellite network systems fully realizable, meeting new services and application requirements, a complete system optimization is needed spanning the different layers of the OSI, and TCP/IP protocol stack. This paper deals with the cross-layer approach to be adopted in novel satellite systems and architectures. Different cross-layer techniques will be discussed, addressing the interactions among application, transport, MAC and physical layers. The impacts of these techniques will be investigated and numerical examples dealing with the joint optimization of different transport control schemes and lower layers will be considered referring to a geostationary-based architecture. Our aim is to prove that the interaction of different layers can permit to improve the higher-layer goodput as well as user satisfaction. Copyright # 2006 John Wiley & Sons, Ltd.