Recent large-scale studies of the human transcriptome suggest that there are much more abundant noncoding transcripts than previously excepted. Many noncoding RNAs in cells lack a canonical poly(A) tail, which suggests that Oligo(dT) resin is not appropriate to be used to enrich noncoding RNAs. eIF4E is a eukaryotic translation initiation factor involved in directing ribosomes to the cap structure of RNAs, included noncoding RNAs. Here we show that using eIF4E resin which expressed in prokaryote could enrich noncoding RNAs in the RNA isolation and obtain a much better result than that of Oligo(dT). The eIF4E protein provides an important tool to isolate and find noncoding RNAs effectively.