The present invention relates particularly to photovoltaic systems for use in photovoltaically generating electrical energy. One aspect of the invention is a photovoltaic roofing system including a plurality of photovoltaic elements contiguously disposed on a roof deck arranged in at least two horizontal rows, defining a photovoltaic area; a plurality of roofing elements disposed adjacent the contiguously-disposed photovoltaic elements, along their side edges; side flashing disposed along the side edges of the contiguously-disposed photovoltaic elements, the side flashing having a flange facing away from the photovoltaic area at least partially disposed between a roofing element and the roof deck, and a structure at least partially disposed on the surface of the photovoltaic element or at least partially disposed between a photovoltaic element and the roof deck.