Studies of mammalian evolution frequently use data derived from the dentition. Dental characters are particularly central for inferring phylogenetic relationships of fossil taxa, of which teeth are often the only recovered part. The use of different aspects of dental morphology as phylogenetic signals implies the independence of dental characters from each other. Here we report, however, that, at least developmentally, most dental characters may be nonindependent. We investigated how three different levels of the cell signalling protein ectodysplasin (Eda) changed dental characters in mouse. We found that with increasing expression levels of this one gene, the number of cusps increases, cusp shapes and positions change, longitudinal crests form, and number of teeth increases. The consistent modification of characters related to lateral placement of cusps can be traced to a small difference in the formation of an early signalling centre at the onset of tooth crown formation. Our results suggest that most aspects of tooth shape have the developmental potential for correlated changes during evolution which may, if not taken into account, obscure phylogenetic history.