A big step in the neurobiology of Drosophila would be to establish a standard for brain anatomy to which to relate morphological, developmental and genetic data. We propose that only an average brain and its variance would be a biologically meaningful reference and have developed an averaging procedure. Here, we present a brief outline of this method and apply it to the optic lobes of Drosophila melanogaster wild-type Canton S. Whole adult brains are stained with a fluorescent neuropil marker and scanned with the confocal microscope. The resulting three-dimensional data sets are automatically aligned into a common coordinate system and intensity averages calculated. We use effect-size maps for the fast detection of differences between averages. For morphometric analysis, neuropil structures are labelled and superimposed to give a three-dimensional probabilistic map. In the present study, the method was applied to 66 optic lobes. We found their size, shape and position to be highly conserved between animals. Similarity was even higher between left and right optic lobes of the same animal. Sex differences were more pronounced. Female optic lobes were 6% larger than those of males. This value corresponds well with the higher number of ommatidia in females. As females have their additional ommatidia dorsally and ventrally, the additional neuropil in the medulla, lobula and lobula plate, accordingly, was found preferentially at these locations. For males, additional neuropil was found only at the posterior margin of the lobula. This finding supports the notion of male-specific neural processing in the lobula as described for muscid and calliphorid flies.