We report the results of the first two 5 GHz e-VLBI observations of the X-ray binary Cygnus X-3 using the European VLBI Network. Two successful observing sessions were held, on 2006 April 20, when the system was in a quasi-quiescent state several weeks after a major flare, and on 2006 May 18, a few days after another flare. At the first epoch we detected faint emission probably associated with a fading jet, spatially separated from the X-ray binary. The second epoch in contrast reveals a bright, curved, relativistic jet more than 40 milliarcseconds in extent. In the first, and probably also second epochs, the X-ray binary core is not detected, which may indicate a temporary suppression of jet production as seen in some black hole X-ray binaries in certain X-ray states. Spatially resolved polarisation maps at the second epoch provide evidence of interaction between the ejecta and the surrounding medium. These results clearly demonstrate the importance of rapid analysis of long-baseline observations of transients, such as facilitated by e-VLBI.