Long non-coding RNAs (lncRNAs) constitute a large and diverse class of non-coding RNA genes. While several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA datasets. Here, we present a novel integrated database of 21,488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: CPC and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia (http://www.lncipedia.org) is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate both small- and large-scale lncRNA studies. As an example, the lncpedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.