Mammalian genomes are pervasively transcribed generating thousands of long noncoding RNAs (lncRNAs) with emergent regulatory roles. Many of these lncRNAs exhibit highly specialised expression patterns during development and typically flank and regulate key developmental factors. In this review, we discuss and summarise the latest advances in our understanding of the roles of lncRNAs during mesendoderm (ME) specification, a key step during gastrulation and the formation of the primitive streak (PS).