We show that three-body loss of trapped atoms leads to sub-Poissonian atom-number fluctuations. We prepare hundreds of dense ultracold ensembles in an array of magnetic microtraps which undergo rapid three-body decay. The shot-to-shot fluctuations of the number of atoms per trap are sub-Poissonian, for ensembles comprising 50-300 atoms. The measured relative variance or Fano factor F=0.53+/-0.22 agrees very well with the prediction by an analytic theory (F=3/5) and numerical calculations. These results will facilitate studies of quantum information science with mesoscopic ensembles.