The growing amount of knowledge about noncoding RNA molecules indicates their major role in regulation of cellular processes. For a long time there was no method which would allow for massive identification and analysis of such kind of transcripts. In recent years, the ongoing explosion of high throughput sequencing methods allowed a deep look into the transcriptome via the cDNA library analysis techniques, like RNA-seq. Since most of such protocols has been aimed for mRNA expression profiling, their adaptation for noncoding RNA research is necessary. It is mainly caused by differences in structure and properties of those two gropus of transcripts. In this article, the main difficulties and challenges in investigation of noncoding RNAs with high throughput sequencing methods will be discussed.