Abstract: Disclosed herein is a method of selectively labeling non-messenger RNA molecules by isolating total RNA from a tissue or cell, dissolving the isolated RNA, blocking the 3? end of the RNA and adding T4 RNA ligase and a labeled nucleic acid adaptor. With the results that the T4 RNA ligase ligates the adaptor only to RNA having a 5? phosphate group and only small RNA are labeled. A method of labeling the 5? end of mRNA isolates total RNA from a tissue or cell, dissolving RNA in RNase-free water, removing a 5? cap structure from the mRNA using tobacco acid pyrophosphatase (TAP), removing the TAP, blocking the 3? end of the RNA molecules; and ligating an adaptor to the RNA by adding T4 RNA ligase and a labeled DNA or RNA adaptor.