While microRNAs represent a well studied part of the non-coding genome, long non-coding transcripts are much more intricate, and are likely to contain as yet unidentified classes of molecules forming transcriptional regulatory networks. Long non-coding RNAs (ncRNAs) have long been considered as negative regulators, promoting chromatin silencing, but recently, several studies pointed out a role for a class of long ncRNAs in positive regulation of protein coding genes (Ørom et al., 2010, Lai et al., 2013) . In order to identify long ncRNAs that could be involved in testis or ovary differentiation, a high throughput RNA sequencing project was initiated in the bovine species. Strand-orientated libraries were prepared from transcripts of early testes and ovaries and next generation sequencing technologies (NGS) were used to identify all RNAs (coding and non-coding) expressed at this early stage in gonads (RNA-sequencing). As a first part, our attention has been focused on loci known to enclosed sex determining genes, to highlight putative regulatory function of long ncRNAs. Indeed, these NGS data may participate to the characterization of crucial regulatory regions. In addition, large scale characterization of all long non-coding RNAs differentially expressed in fetal ovaries or testes is in progress. Up to now, 5242 loci (coding and non-coding) have been showed to be differentially transcribed (pValue <0.01). Nevertheless Cufflinks bioinformatic tool, that was used to rebuild the transcripts, is not efficient enough to correctly characterized one entire transcription unit: one unit may be represented by several transcribed loci that must be clustered. Consequently, long non coding RNAs characterization has to be completed by manual annotation, using IGV visualization tool, in order to perform new round of differential analyses.