The Kato-Katz technique is the method routinely used for diagnosing human schistosomiasis mansoni by estimating faecal egg burdens. To improve the sensitivity of faecal diagnosis, we established and validated a novel separation technique based upon the greater density of viable schistosome eggs relative to faecal material. Subsequently, it was used for faecal examination of 27 schistosomiasis patients in El-Sharkia, Egypt, with Kato-Katz smears as criterion standard. Low intensity infections (<100 eggs/g) were only detected by our technique. Moreover, triple Kato-Katz analysis on consecutive samples still missed 7.4% of all human patients, whereas the new method diagnosed 100% of samples correctly on second analysis. We conclude that in endemic areas many patients are being systematically missed by routine diagnosis. Moreover, the sensitivity of our method allows its use in proposed pre-clinical and clinical vaccine trials in non-human primates and humans, where reliable estimates of faecal egg counts are essential.