Objectives We expand upon a multivariate mixed model from quantitative genetics in order to estimate the magnitude of climate effects in a global sample of recent human crania. In humans, genetic distances are correlated with distances based on cranial form, suggesting that population structure influences both genetic and quantitative trait variation. Studies controlling for this structure have demonstrated significant underlying associations of cranial distances with ecological distances derived from climate variables. However, to assess the biological importance of an ecological predictor, estimates of effect size and uncertainty in the original units of measurement are clearly preferable to significance claims based on units of distance. Unfortunately, the magnitudes of ecological effects are difficult to obtain with distance‐based methods, while models that produce estimates of effect size generally do not scale to high‐dimensional data like cranial shape and form. Methods Using recent innovations that extend quantitative genetics mixed models to highly multivariate observations, we estimate morphological effects associated with a climate predictor for a subset of the Howells craniometric dataset. Results Several measurements, particularly those associated with cranial vault breadth, show a substantial linear association with climate, and the multivariate model incorporating a climate predictor is preferred in model comparison. Conclusions Previous studies demonstrated the existence of a relationship between climate and cranial form. The mixed model quantifies this relationship concretely. Evolutionary questions that require population structure and phylogeny to be disentangled from potential drivers of selection may be particularly well addressed by mixed models. Am J Phys Anthropol 160:593–603, 2016. © 2015 Wiley Periodicals, Inc.