Identification, detection, and use of small-ribonucleic acid (RNA) molecules have been paid increasing attention in the past decades. Here we show studies of two interrelated lines of this research in a sperm maturation-related organ, the epididymis. First, by using microarray and small-RNA library screening systems, a series of spatially and temporally regulated known and novel small regulatory RNA molecules, referred to as microRNAs, has been identified and characterized. Second, small double-stranded RNAs, called small interfering RNAs, emerged as a powerful tool to knock down gene expression by a pathway known as RNA interference. It has been successfully used to silence epididymal gene expression in vivo to elucidate the function of several sperm motility- and capacitation-related proteins in the rat epididymis.