High-throughput sequencing results in recent decades have revealed that transcription of the eukaryotic genome goes beyond coding regions and uncovered an overwhelming amount of novel functional RNAs. The list of these RNAs is constantly increasing and includes lncRNAs, circular RNAs and enhancer RNAs, among others, with crucial roles in genome organization, transcriptional and posttranscriptional gene regulation. The basic mechanisms of action of these RNAs are only beginning to emerge and are most likely exhibited due to specific RNA secondary and tertiary structure, as previously found for other RNAs, e.g. ribosomal RNAs and tRNAs. Nevertheless, the connection between RNA structural biology and RNA function is still in its infancy. To deeply understand how molecules work, detailed knowledge of their structures is necessary.