Ocean acidification, the reduction of ocean pH due to the absorption of anthropogenic atmospheric CO2, is expected to influence marine ecosystems through effects on marine calcifying organisms. These effects are not well understood at the community and ecosystem levels, although the consequences are likely to involve range shifts and population declines. A current focus in ocean acidification research is to understand the resilience that organisms possess to withstand such changes, and to extend these investigations beyond calcification, addressing impacts on other vul- nerable physiological processes. Using morphometric methods and gene expression profiling with a DNA microarray, we explore the effects of elevated CO2 conditions on Lytechinus pictus echino- plutei, which form a calcium carbonate endoskeleton during pelagic development. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2. Morphometric analysis showed significant effects of enhanced CO2 on both size and shape of larvae; those grown in a high CO2 environment were smaller and had a more triangular body than those raised in normal CO2 con- ditions. Gene expression profiling showed that genes central to energy metabolism and biomineral- ization were down-regulated in the larvae in response to elevated CO2, whereas only a few genes involved in ion regulation and acid-base balance pathways were up-regulated. Taken together, these results suggest that, although larvae are able to form an endoskeleton, development at elevated CO2 levels has consequences for larval physiology as shown by changes in the larval transcriptome.