The availability of genome-wide RNAi libraries has enabled researchers to rapidly assess the functions of thousands of genes; however the fact that these screens are run in living biological systems add complications above and beyond that normally seen in high-throughput screening (HTS). Specifically, error due to variance in both measurement and biology are large in such screens, leading to the conclusion that the majority of "hits" are expected to be false positives. Here, we outline basic guidelines for screen development that will help the researcher to control these forms of variance. By running a large number of positive and negative control genes, error of measurement can be accurately estimated and false negatives reduced. Likewise, by using a complex readout for the screen, which is not easily mimicked by other biological pathways and phenomena, false positives, can be minimized. By controlling variance in these ways, the researcher can maximize the utility of genome-wide RNAi screening.