Multiple plasma membrane-associated microtubule-organizing centers operate in the cone cells of Drosophila ommatidia. A transcellular array of about 250 microtubules assembles in each cone cell during late pupal ommatidial morphogenesis. While these arrays are assembling, cone cells do not possess conventional centriole-containing centrosomal microtubule-organizing centers. The microtubules are associated with plasma membrane-associated plaques at both the apical and basal surfaces. During assembly of the arrays there is a progressive decrease in the number of microtubules/cell cross section at successively lower levels in each cell which is indicative of apicobasal microtubule elongation. In this respect, assembly of the arrays closely resembles that of transcellular 15 protofilament microtubules in late pupal wing cells (Mogensen et al. J. Cell Biol. 108, 1445-1452 (1989)). However, cone cell microtubules are almost certainly of the 13 protofilament variety as found in eukaryotic cells generally. We suggest that plasma membrane-associated microtubule-organizing centers are widely employed in polarized epithelia in Drosophila during late pupal morphogenesis.