Untranslated mRNA regions(UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5''UTRs, the vast majority of which have unknown function. We present a systematic analysis of the translation and function of upstream open reading frames(uORFs) across vertebrates. Combining high-resolution ribosome footprinting and phasing, we find that i) uORFs are pervasive within vertebrate transcriptomes, ii) the majority show signatures of active translation, and iii) uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Evolution has targeted sequence features to mitigate the effects of constitutively repressive uORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.The mRNA-seq data contained in this archive were used along with ribosome profiling data to calculate translation efficiency values.