Researchers whose experimental models are mammalian oocytes and preimplantation embryos are often limited by the yield of nucleic acids that can be isolated from such a small sample size. In addition, the limited number of cells from these types of samples makes the simultaneous recovery of RNA and DNA very difficult and often sample pooling is necessary to increase nucleic acid yield. Here we report a simple set of procedures using commercially available kits that results in consistent yield and quality of nucleic acids. After sample lysis, RNA is isolated and converted to a reusable cDNA library. Following RNA isolation, DNA is precipitated, isolated, and bisulfite converted for DNA methylation studies. Our results demonstrate the feasibility of isolating RNA and DNA from a small number of cells with repeatability of results.