Two of the most promising and complex areas in biologics development, either as research tools or potential therapeutics, are cell-penetrating peptides (CPPs) and RNA interference (RNAi) modulators. Consequently, the combined application of these technologies in pursuit of improved delivery profiles for RNAi cargoes presents its own unique challenges. Direct access to the targeted tissue is luxury not always available to the researcher; however, the example of lung presents an excellent opportunity for presenting methodologies relevant to understanding the local impact of CPP-conjugated RNAi modulators. This chapter therefore expands upon updated protocols established on the study of the function of endogenous RNAi and the utility of CPPs in the delivery of short interfering RNA (siRNA) to therapeutically relevant cells in the lung. Methods for sample collection, preservation, and processing are provided with a view to facilitate qualitative and quantitative analysis of delivery. In addition, a protocol for mapping siRNA delivery by in situ hybridisation is provided.