The sensitivity of new transcriptomic techniques is rapidly improving to the point that single-cell molecular analysis is now becoming commonplace. However to obtain accurate transcriptome data, the initial experimental steps must strive to maintain the natural environment of cell and always get set in motion under in vivo conditions. Achieving these critical experimental parameters is technically challenging for investigators and currently the most frequently used molecular techniques experimentally commence with tissues or cells in artificial environments or under in vitro conditions. Here we review an innovative experimental approach that is called transcriptome in vivo analysis (TIVA) that was designed to overcome theses well-known limitations. The TIVA methods permit cell-specific transcriptome capture from viable intact heterogeneous tissues. Cell-penetrating peptides (CPPs) are used to deliver multifunctional transcriptome-capture tags (TIVA tags) to the cytoplasm of the cell under in vivo conditions. The TIVA capture tag enables investigators to target and isolate cell-specific transcriptomes in their natural microenvironments. The combination of maintaining in vivo conditions and selective cell-specific transcriptome capture provides investigators with the opportunity to yield the most biologically accurate and informative transcriptome data hitherto.