Our understanding of regulatory processes at the level of cellular RNAs lags far behind our understanding of transcriptional control at the DNA level. Ingolia et al. have used profiling of the position of ribosomes on RNAs to characterize RNA translation in mouse embryonic stem cells. Using the drug harringtonine to stop translation during the first rounds of peptide elongation, the authors were able to accumulate ribosomes at sites of translation initiation. Forty-four percent of the initiation sites they identified were unannotated. In many cases, they predict the production of N-terminally truncated forms of known proteins, but also the translation of parts of the 5´-untranslated region. Initiation of the upstream open reading frames was frequently observed at non-AUG codons. Which of these sites leads to productive protein production remains to be determined by alternative methods. The authors also identify sequences that cause pronounced pausing during peptide elongation and show that no substantial pausing occurs at rare codons. Small RNAs are also frequently covered with ribosomes, suggesting that they might be translated into proteins instead of, or in addition to, other regulatory functions. (Cell 147, 789–802, 2011)