We investigate the inhibited emission of light-emitters embedded in finite, three-dimensional woodpile (or stacked-striped) photonic crystals (PCs) that exhibit structural fluctuations. Finite-difference time-domain calculations reveal that the influence of the positional fluctuations of stacked rods of dielectric material depends on the total number of structural periods. For PCs with up to nine stacked layers, the inhibition of emission is principally determined by intruding free-space modes resulting from the finite nature of the structure, with little influence from fluctuations. In PCs with more periods, the modes resulting from fluctuations dominate the emission properties. The influence of these fluctuations is strongly suppressed when the positional shifts are less than 20%. (C) 2009 Optical Society of America