Small RNAs are found in eukaryotes and are responsible for regulation of chromatin structure, RNA processing and stability, translation and transcription. 24-nt small interfering RNA (siRNA) are known to mediate gene inactivation via the RNA-directed DNA methylation pathway (RdDM) and are important for natural heritable changes in plant species. DNA cytosine methylation can be maintained between generations and this may be important for accelerated adaption to stress conditions. Research is currently focused toward the epigenetic response to disease, the stability of DNA methylation over generations, the elucidation of newly discovered pathways for de novo DNA methylation, and the application of epigenetic variation to breeding programs. This review aims to give a brief but comprehensive examination on small RNAs and transgenerational epigenetic variation.