There is a growing interest in the use of cell-penetrating peptides (CPPs) as carriers for transepithelial drug delivery. This chapter gives an introduction to and discussion of the commonly used production and characterization methods for CPP–cargo samples including high-throughput cell viability screening. Moreover, we describe methods for permeation and cell viability assessment in the Caco-2 cell culture model with and without implementation of biosimilar mucus. Last, a method to assess metabolic degradation in vitro is described.