The structure of Ba2Nb5O9 can be described as intergrown layers of perovskite (BaNbO3) and NbO. The compound is a member of the BanNbn+3mO3(n+m) homologous series where n and m are the perovskite and NbO slab widths, respectively. The substitution of Zr for Nb according to the formula Ba2Nb5−xZrxO9 has been investigated. The increase of the c axis length as a function of the overall composition shows, in combination with microanalysis in scanning and transmission electron microscopes, that the maximum value of x is approximately 0.6. The microanalysis indicates that Zr prefers the MO6 octahedra in the perovskite slab. The X-ray powder diffraction (XRD) analysis and high-resolution electron microscopy (HREM) images show that for 0.6≤x≤1.5 a disordered intergrowth of Ba(Nb;Zr)O3 and NbO layers is formed. The XRD patterns and microanalyses of cation content showed that a new homologue Ba3(Nb,Zr)6O12 with n:m=3:1 in the series Ban(Nb;Zr)n+3mO3(n+m) is formed in some of these samples. It has the unit cell parameters a=4.1725(6) Å and c=16.429(3) Å and crystallises in space group P4/mmm, Z=1. The structure of this compound was determined by comparing simulated and experimental HREM images.