MOTIVATION: Sample size calculation is important in experimental design and is even more so in microarray or proteomic experiments since only a few repetitions can be afforded. In the multiple testing problems involving these experiments, it is more powerful and more reasonable to control false discovery rate (FDR) or positive FDR (pFDR) instead of type I error, e.g. family-wise error rate (FWER). When controlling FDR, the traditional approach of estimating sample size by controlling type I error is no longer applicable. RESULTS: Our proposed method applies to controlling FDR. The sample size calculation is straightforward and requires minimal computation, as illustrated with two sample t-tests and F-tests. Based on simulation with the resultant sample size, the power is shown to be achievable by the q-value procedure. AVAILABILITY: A Matlab code implementing the described methods is available upon request.