The NETWORK-ON-CHIP (NOC) interconnection paradigm has been gaining momentum thanks to its flexibility, scalability and suitability to deep submicron technology processes. The next challenge is to use NoCs as the backbones of the upcoming generation of 3D chips, assembled by stacking multiple silicon layers. Multiple technical issues have to be tackled in this respect. One of the foremost is the unsuitability of a purely synchronous design style, as it is not straightforward to impose a strict bound on the clock skew among multiple clock trees across different layers. In this paper, we present a scheme to handle mesochronous communication in 3D NoCs and analyze (i) the circuit design, (ii) the timing properties, (iii) the requirements to support flow control across mesochronous links, (iv) the implementation cost of such a scheme after placement and routing.