The application of quantitative methods has long been the norm in comparative and evolutionary studies of morphology, but within the field of experimental embryology mathematical descriptions of anatomical form are seldom calculated, and morphological variation within treatment groups is rarely taken into account. Here we argue that many of the analytical techniques that are commonly applied in other areas of morphological research are also well suited for experimental studies of anatomical development. The application of these methodologies shows promise for augmenting such endeavors by enhancing researchers' ability to detect morphological patterns, account for developmental variation, and employ statistical methods. We review selected studies of experimental morphogenesis that underscore the potential of quantitative methods to reveal important aspects of anatomical development and growth. These examples demonstrate the benefits of quantifying ontogenetic data and accounting for developmental variation, and we suggest that the adoption of such practices by researchers performing experimental studies of morphogenesis will enhance our understanding of the processes by which genetic changes affect anatomical formation.