Transition metal perovskite oxides are of lasting interest due to the functional physical properties exhibited by some of them like, high temperature superconductivity (HTSC), colossal magnetoresistance (CMR), multiferroics so on. Barium metal ruthenates possess unusual 4d magnetism with an exotic crystal structure (layered hexagonal structure). Several polymorphs of these could be produced by the effect of pressure. The magnetic ions are closer to each other in the edge shared octahedra of these compounds. This proximity of magnetic ions in its structure makes this system magnetically important. Ba3CoMxRu2-xO9 system with M as a 3d transition metal is exciting due to novelty in barium ruthenates with three B-site ions. Bilayer Ruddlesden- Popper perovskites Sr3Ru2O7 being another such modulated system with interesting properties such as competing FM and AFM interactions at low temperatures is a potential candidate for giant exchange bias phenomenon and other exotic properties. In the present talk the effect of structural modulation on the magnetic and transport properties of B-site doped ruthenium based ternary perovskites and Ruddlesden Popper type layered perovskites will be discussed.