The field of morphometrics has developed fast over the last two decades. After a ‘‘revolution’’ that established a new ‘‘synthesis’’ in morphometric methodology about 15 years ago (Rohlf and Marcus 1993; Bookstein 1996), the focus has recently shifted to applying this methodology to various biological problems. In his review, Polly (2008) singles out quantitative genetics for special mention. In this area, morphometric methods have been applied in the context of analyses that base genetic inference on resemblance among relatives (Klingenberg and Leamy 2001; Myers et al. 2006) and analyses of natural selection (Gomez et al. 2006), which both use the additive genetic covariance matrix, or G matrix, as a central quantity, as well as QTL studies that aim to identify the effects of single loci (Liu et al. 1996; Klingenberg et al. 2001). All these studies share a common approach in that they use the variables derived from a morphometric space to characterize shape. These variables are then used as the data in the context of the classical multivariate methods of quantitative genetics, as they have been available for 20 years or more (e.g., Lande 1979; Lande and Arnold 1983; Lynch and Walsh 1998). None of this is inherently revolutionary, as it is mainly a question of ‘‘plugging in’’ a new type of data into established methods (perhaps with minor changes of the algebra). One might be tempted to say that the most surprising thing is that it took morphometricians so long to apply shape data in these contexts. The article of Polly (2008) discusses a further body of literature, which is concerned with the developmental origins of evolutionary novelties (e.g., Oster et al. 1988; Alberch 1989; Salazar-Ciudad et al. 2003). This kind of study focuses on developmental and morphological variation at a scale where the local approximation by the linear models that underlie quantitative genetics is no longer satisfactory. Instead of small steps in phenotypic space, evolution of novelty can occur by large leaps. As a consequence, morphological changes are not necessarily just minor rearrangements of a constant set of morphological features, but entirely novel features can arise. Because standard morphometric methodology requires a strict correspondence of the landmarks or measured distances among all taxa under study, it presents considerable difficulties for analyzing variation of this sort. Therefore, Polly (2008) suggests that novelty is best analyzed by what he calls ‘‘homology-free’’ characterizations of the phenotype. These characterizations include analyses of outlines or surfaces that do not require the user to establish an explicit correspondence of structures as it is required, for instance, for analyses of morphological landmarks. These ‘‘homology-free’’ approaches easily can accommodate even drastic changes of shape, where no apparent correspondence of shapes is maintained. Accordingly, these approaches appear to be very suitable for studying morphological novelty (Polly 2008). In this paper, I raise two caveats to this conclusion. First, I point out that for some types of novelty, such as those where novel parts arise by duplication of existing parts, it may well be possible to include them in the standard morphometric analyses using landmarks. This requires an explicit interpretation of the developmental and anatomical change that underlies the novelty, and will thus not always be feasible. Second, I examine whether the ‘‘homologyfree’’ methods recommended by Polly (2008) really are free of assumptions about the correspondence of parts. My survey finds that all these methods are making such C. P. Klingenberg (&) Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK e-mail: cpk@manchester.ac.uk