Developmental mechanisms are usually assumed to evolve by natural selection of the morphological traits they produce. Therefore, information on phenotypic traits is an important component of comparative studies of development. Morphometrics permits the rigorous quantitative analysis of variation in organismal size and shape, and is increasingly being used in developmental contexts. The new methods of morphometrics combine a geometric concept of shape with the procedures of multivariate statistics, and constitute a powerful and flexible set of tools for analyzing morphological variation. This paper briefly reviews these methods and provides examples of their application in studies of genetic variation and developmental modularity. The results of morphometric analyses can be readily interpreted in relation to the geometry and anatomical structure of the parts under study. Genetic studies of shape in the mouse mandible found two recurrent patterns in environmental and genetic variation from different origins, suggesting that the development system 'channels' the phenotypic expression of variation in similar ways. Moreover, by analyzing the correlations of left-right asymmetries of morphometric traits, it is possible to delimit the spatial extent of developmental modules. These methods complement the experimental approaches of developmental biology and genetics, and can be expected to be especially fruitful in combination with them.