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Organisms and organs come in sizes and shapes. With size, science has no problems, but how to quantify shape? How similar are two birds or two brains? This problem is particularly pressing in cases like brains where structure reflects function. The problem is not new, but satisfying solutions have yet to be worked out. For brain anatomy, no general methodology for a statistically secured quantitative description is available. Using the small brain of the fly Drosophila melanogaster, we have explored a new approach combining immunohistochemistry, high-resolution 3D confocal microscopy, and advanced graphics computing. For a genetic model organism such as Drosophila, a quantitative assessment of brain structure is particularly rewarding, since it allows for the identification of genetic variants with subtle brain structure phenotypes and, even more importantly, the organization of the wealth of gene expression patterns in the brain into a genetic atlas linking molecular and organismic gene function. We now provide a representative standard for the brain of D. melanogaster wild-type with means and variances for several aspects of its shape. Its application to volumetry, mutants, and gene expression patterns is demonstrated.