Cell-penetrating peptides (CPPs) are short peptides that facilitate cellular intake and uptake of molecules ranging from nanosize particles to small chemical compounds to large fragments of DNA. The "cargo" is associated with the peptides either through chemical linkage via covalent bonds or through non-covalent interactions.

CPPs deliver the cargo into cells, commonly through endocytosis, for use in research and medicine. Current use is limited by a lack of cell specificity in CPP-mediated cargo delivery and insufficient understanding of the modes of their uptake. Other delivery mechanisms that have been developed include CellSqueeze and electroporation.

CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar, charged amino acids and non-polar, hydrophobic amino acids. These two types of structures are referred to as polycationic or amphipathic, respectively. A third class of CPPs are the hydrophobic peptides, containing only apolar residues with low net charge or hydrophobic amino acid groups that are crucial for cellular uptake.

Transactivating transcriptional activator (TAT), from human immunodeficiency virus 1 (HIV-1), was the first CPP discovered. In 1988, two laboratories independently found that TAT could be efficiently taken up from the surrounding media by numerous cell types in culture. Since then, the number of known CPPs has expanded considerably, and small molecule synthetic analogues with more effective protein transduction properties have been generated.

A recent discovery found that Papillomaviridae, such as the human papillomavirus, use CPPs to penetrate the intracellular membrane to trigger retrograde trafficking of the viral unit to the nucleus.