The whooping cough agent, Bordetella pertussis, secretes the adenylate cyclase toxin-hemolysin (CyaA, ACT, AC-Hly), a major virulence factor that plays a crucial role in bacterial colonization of host respiratory tract. CyaA exhibits two distinct and mutually independent biological activities on CD11b expressing myeloid phagocytic target cells. Firstly, one class of CyaA conformers forms small cation-selective pores that can cause colloid-osmotic (oncotic) lysis of target cells. In parallel, other CyaA conformers translocate the adenylate cyclase (AC) enzyme domain of the toxin across the membrane of target cells, thus effectively subverting the bactericidal functions of cells by unregulated catalysis of cytosolic ATP conversion into cAMP, a key signaling molecule. The dual function CyaA toxin thus belongs to the RTX (Repeats-in-ToXin) family of pore-forming toxins. However, it forms notably smaller pores than other pore-forming toxins from the RTX cytolysin family. Here we investigated the specific segments of CyaA involved in the reduction of the pore conductance and diameter. Using planar lipid bilayers made of DPhPG we examined single pores formed by CyaA and several mutant toxin variants and their pore selectivities. Our results suggest that CyaA pores adopt two distinct states with distinct pore selectivities.