The human genome sequence and that of several model organisms have provided a remarkable view of the fundamental genetic and evolutionary templates that govern the characteristics of living organisms. Yet the real effectors of phenotype are important downstream informational elements represented first in the transcriptome and then in the proteome. This has led to the need for logical experimental strategies for comprehensive characterization of the transcriptome. The complexity of this challenge is vast given the tens-of-thousands of genes expressed at different levels and with alternative transcript forms fluctuating in response to cellular changes. Here, we outline the most recent major technical advances in transcriptome characterization. Owing to the expanse of the topic, we focus in particular on methods of transcript interrogation rather than in silico approaches to transcript determination and provide a brief summary of transcriptional networks.