This paper addresses possible underlying causes of the observed systematic spacings in the carbon isotopic composition of bone collagen and bone apatite-carbonate when herbivores, omnivores and carnivores are compared. In particular it examines whether the observed systematic spacings are due to dietary differences, or to metabolic differences. It concludes that a simple model for diet-to-collagen isotopic fractionation (based on dietary difference) can account for half of the observed spacing, but probably not more than that. It also examines the role of methanogenesis and argues that this is a feasible explanation for ruminant and, to a lesser extent, hindgut fermenter, spacing values, although again it is difficult to account for the full amount observed. It also considers the implications of observations indicating that much of the change due to different diets in a given species is probably due to isotopic shifts in bone carbonate, rather than collagen. Copyright © 2003 John Wiley & Sons, Ltd.