Comparative studies of ontogenies play a crucial role in the understanding of the processes of morphological diversification. These studies have benefited from the appearance of new mathematical and statistical tools, including geometric morphometrics, resampling statistics and general linear models. This paper presents an overview of how resampling methods may be applied to linear models of ontogenetic trajectories of landmark-based geometric morphometric data, to extract information about ontogeny. That information can be used to test hypotheses about the changes (or differences) in rate, direction, duration and starting point of ontogenetic trajectories that led to the observed patterns of morphological diversification.