MicroRNAs and DNA methylation are both critical epigenetic mechanisms for the control of gene expression. The recent explosion of interest in these two areas has led to the development of innovative strategies for the analysis of short RNAs and methylation status, with qPCR established as a leading method for quantification. This talk describes and evaluates the currently available methods used for the quantification of microRNAs and DNA methylation by qPCR and highlights what factors must be taken into consideration in order to achieve optimal data.