We have investigated the extraction of oligosaccharides produced by enzymatic degradation of a bacterial polysaccharide obtained by fermentation of Sinorhizobium meliloti bacteria. We have used a cascade of ultrafiltrations and nanofiltrations with a rotating disk module in order to separate oligoglucuronans of degrees of polymerisation between 3 and 7, which have interesting medical properties. This work confirms the high performance of rotating disk system for the fractionation of complex biotechnological solutions.