Evolutionary developmental biology is inevitably a comparative subject. However, the taxonomic level at which comparisons can be made varies widely, and this greatly affects the kind of information that can be gained from the comparison. Broadly speaking, high-level comparisons (e.g., between phyla) are more informative about phylogenetic pattern and homology, while low-level comparisons (e.g., between congeneric species) are more informative about evolutionary mechanisms, including speciation. However, so far evolutionary developmental biology has had a relatively minor input into the traditional territory of population genetics, namely comparisons within species—both within and between geographic populations. Yet this area is crucial, as all evolutionary novelties ultimately arise from intraspecific variation. Here, I address this issue, focusing on the question of how early in development novelties arise. To shed light on this question, I discuss two examples of developmental polymorphism within species involving two of the main body axes: anteroposterior segmentation in centipedes and left–right asymmetry (chirality) in gastropods.