The interaction between amphiphiles and polyelectrolytes has been widely investigated in recent years due to their potential application in industry and medicine, with special focus on gene therapy. The cationic lipid di-oleoyl trimethylammonium propane, DOTAP, and the oppositely charged polyelectrolytes, sodium poly(acrylic acid) and sodium poly(styrenesulfonate), form multilamellar complexes in water. Due to the different molecular stiffness of the two polyelectrolytes, they form different nanostructured complexes. Also, because of different ionization behavior of the two polyelectrolytes, pH affects differently the complexation of the polyelectrolytes with didodecyldimethyl-ammonium bromide (DDAB), another cationic surfactant. We used cryogenic temperature transmission electron microscopy (cryo-TEM) and small-angle x-ray scattering (SAXS) to compare the nanostructures formed in those systems. Our results show that although the basic nanostructures of the complexes are always lamellar (multilamellar or unilamellar), the morphology of the complexes is affected by the polyelectrolyte rigidity and the solution pH. The work has been extended to the study of the complexation of protein with cationic lipid, an important issue for gene therapy.