Tests of adaptive explanations are often critically confounded by phylogenetic heritage. In this paper we propose statistics and a null model for estimating phylogenetic effects in comparative data. We apply a model-independent measure of autocorrelation (Moran's I) for estimating whether cross-taxonomic trait variation is related to phylogeny. We develop a phylogenetic correlogram for assessing how autocorrelation varies with patristic distance and for judging the appropriateness and effectiveness of an autoregressive model. We then revise Cheverud et al.'s (1985, Evolution, 39:1335–1351) autocorrelational model to incorporate greater flexibility in the relation between trait variation and phylogenetic distance. Finally, we analyze various comparative data sets (body weight in carnivores, clutch size in birds) and phylogenies (morphological, molecular) to illustrate some of the complications that may arise from using an autoregressive model and to explore the effects of different weighting matrices in adjusting for these complications. Although our approach has limitations, it is both effective in partitioning trait variation into adaptive and phylogenetic components and flexible in adjusting to peculiarities in taxonomic distribution.