What used to be gills are our jaws, inner ears, and eustachian tubes.
All vertebrate embryos look pretty much alike. They all develop a structure called the pharyngeal pouches. These are exactly the same structure in all early vertebrate embryos. They are in the exact same position in all early vertebrate embryos. In jawless fish, these pharyngeal pouches develop into gills. In mammals, these pharyngeal pouches develop into the jaws and inner ear.
No, humans don't have gills. But we do have structures homologous to gills, namely our jaws and the bones of our inner ears.
Check it out.