High throughput screening continues to present a common statistical challenge as the number of statistical comparisons vastly exceeds that of the biological replicates. Statisticians have developed methods for such large data sets, including the Bonferroni adjustment, FDR1 and the recent optimal discovery procedure (ODP)2. We detail here the statistical protocol employed for a genome-wide RNAi-based synthetic lethal screening study3. A straightforward combination of both FDR control and fold change criteria identifies a highly reproducible list of hits. Preliminary comparison between this readily implemented method and other recently developed methods (such as ODP’s) shows good properties for this practical approach4.