Human immunodeficiency virus type 1 (HIV-1) utilizes CD4 as a primary receptor for viral entry and any of several 7-transmembrane chemokine receptors, including CCR5, as a co-receptor. Previous studies have demonstrated that multiple extracellular domains (ECDs) of CCR5 contribute to co-receptor function; here we applied genetic footprinting to CCR5 to confirm and extend those investigations. In genetic footprinting, a duplex oligonucleotide is inserted into the DNA sequence of interest by use of either a bacterial transposase or retroviral integrase. Here, CCR5 mutants were analyzed in bulk for their ability to be expressed on the recipient cell surface and to mediate viral entry of R5 HIV isolates. Most of the approximately 150 CCR5 mutants were not expressed on the cell surface. Of those remaining, 8 were specifically reduced or absent after macrophage (M)-tropic HIV infection, confirming a critical role of ECDs three (extracellular loop 2 or ECL2) and possibly four (ECL3) in viral entry. Mutational and functional analyses of ECD4 (ECL3) suggest it is under severe topological constraint for CCR5 surface expression and are consistent with it contributing to co-receptor function.