Recent developments of microarrays and deep sequencing techniques have unveiled an unexpected complexity of the eukaryotic transcriptome, demonstrating that virtualy the entire genome is transcribed by RNA polymerase II (RNAPII). Transcription occurring outside of annotated regions is generally referred to as pervasive transcription and leads to the production of several classes of non-coding RNAs (ncRNAs). In this review we will discuss the metabolism and functional significance of these ncRNAs in the yeast Saccharomyces cerevisiae. We will discuss the mechanisms that the cell has adopted to prevent potentially disruptive interference between pervasive transcription and the expression of canonical genes. We will explore the possible reasons that justify the evolutionary conserved maintenance of extensive genomic transcription.