Photovoltaic properties of two-layer organic pin junction solar cells were studied for vacuum-deposited films of p-type phthalocyanine derivatives having different pi-electron conjugating macrocycles and n-type N,N’-substituted 3,4:9,10-perylenebis(dicarboximide) having different peripheral groups. The power conversion efficiency was optimized by controlling the film thickness, morphology and contact with top-electrodes. The film morphology of the perylene derivatives changed depending on their peripheral alkyl groups, and higher photocurrents were obtained for the cell with a homogeneous layer of perylene derivatives. The molecular modification in p-type phthalocyanine derivatives changed the cell photovaltage. A substitution with electron-withdrawing groups, which lowered the highest occupied molecular orbital (HOMO) energy of the p-type molecules, increased the photovoltage. On the other hand, an extention of the macrocyclic ring from phthalocyanine to naphthalocyanine lowered the photovoltaic efficiency.