The miRCat system permits cloning of very rare small RNAs and takes into account the natural variability in structure and sequence between species. It is compatible with most existing standard laboratory protocols for processes such as RNA extraction, purification and cloning. Based upon a pre-activated adenylated oligonucleotide linkering method, the system makes small RNA library creation easy. It consists of three sequential protocols: RNA isolation and enrichment, followed by cloning linker attachment, and ending with an amplification and cloning phase. The system can be used for concatamer cloning or direct shotgun cloning; it also can provide PCR amplicons suitable for use with TOPO TA Cloning or pGEM T-Easy cloning vectors.