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 disposed on a roof deck. The photovoltaic roofing system includes one or more photovoltaic elements contiguously disposed on the roof deck, the contiguously-disposed photovoltaic elements 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 cross-sectional shape comprising a vertically-extending feature and a flange extending from each lateral side at the bottom of the vertically-extending feature, with the flange facing the photovoltaic area being at least partially disposed between a photovoltaic element and the roof deck, and the flange facing away from the photovoltaic area being at least partially disposed between a roofing element and the roof deck.