In vivo footprinting techniques are used for mapping protein-DNA contacts in mammalian cells at high resolution. The sensitivity needed to analyze single-copy genes is achieved by combining these techniques with the ligation-mediated polymerase chain reaction (LMPCR). Three different in vivo footprinting strategies are described that have been used successfully in conjunction with LMPCR: footprinting with dimethylsulfate, treatment of permeabilized cells with DNase I, and UV photo-footprinting. The choice of the method will mostly depend on the particular biological questions that are addressed and the sequences that are analyzed. In many cases, the combined use of several methods will provide the most informative and complete picture. We also include a review of the published literature on in vivo footprinting for analysis of chromatin structure. We summarize data that have been obtained on static, dynamic or cell type specific protein binding at promoters and enhancers and emphasize several examples in which factors, although present in the nucleus, are excluded from binding because of chromatin inaccessibility.