Gene expression profiling to analyze cellular responses against different stimuli or conditions is generally performed at the total cellular RNA level. This results in poor resolution of the temporal kinetics of the cellular response and a bias towards detecting up-regulation of short-lived transcripts. Furthermore, changes in transcription rate and RNA stability cannot be distinguished. These problems can be addressed by analyzing nascent RNA instead of total cellular RNA. Throughout the last few years methods have been developed for metabolic tagging and purification of nascent RNA. In this article, we review these experimental procedures and discuss their implications for large-scale gene expression profiling.