Environmental ecotoxicology studies use sea urchin skeletal components to examine potential changes in concentrations of trace element pollutants. To date, such studies have not considered how body size may alter the innate concentrations of trace elements in a given skeletal component. The present study examines this issue using the common nearshore sea urchin Lytechinus variegatus as a model species. Concentrations of barium, boron, manganese, and strontium was measured using ICP-OES in three major skeletal subcomponents (Aristotle's lantern, spines, and test) of individuals' representative of five size cohorts spanning the late juvenile to adult. Concentrations of three of the four elements, barium, boron, and manganese, varied significantly with body size, largely declining as test diameter increased. As concentrations of trace elements was normalized to skeletal mass originated from collections of individuals in pristine bay waters and from the same population at the same time, differences in trace element concentrations are innately ontogenetic. Accordingly, future ecotoxicological studies employing skeletal subcomponents of sea urchins should consider the relationship between trace element concentration and body size when designing sampling regimes.