Recent genome-wide analyses revealed that eukaryotic genomes are almost entirely transcribed, generating a large number of short or long non-protein coding RNAs (non-coding RNAs; ncRNAs). Rapidly accumulating experimental evidence suggests that ncRNAs are not just transcriptional noise, but have biological roles in gene expression. In this review, we focus on the functions of nuclear-localized ncRNAs including the spliceosomal small nuclear RNAs. These nuclear ncRNAs play diverse regulatory roles in a wide-range of nuclear reactions, such as transcription, precursor-mRNA (pre-mRNA) splicing, nuclear structure formation, nuclear trafficking, and chromatin remodeling. The regulatory functions of ncRNAs in these reactions are reinforced by target-site recognition through base-pairing or formation of an RNA/DNA triple helix. Recent studies revealed an unexpected linkage between the machineries for RNA interference (RNAi)-mediated gene silencing and pre-mRNA splicing. In addition, the biogenesis of some ncRNAs was found to overlap with the pathway of pre-mRNA splicing. Our understanding of the mechanisms of coordinated gene regulation in the nucleus has increased dramatically through studies on nuclear ncRNAs. A new paradigm of "ncRNA regulation" is now emerging.