Metazoan development is a complex, tightly regulated biological process. It is so highly regulated, in fact, that the same basic developmental toolkit is used by most metazoans. However, in spite of this complexity and regulation, small changes in the developmental program can have profound impacts on the overall fitness and development of an organism. Variation among individuals is a key feature of biological systems and is important evolutionary adaptation. Although variation has long been studied as a source for evolutionary potential, there is still much we do not know concerning the relationship to variations in gene expression and their effect on interindividual variation at the phenotypic level. This thesis examined physiological variation in a variety of invertebrate embryos and larvae. Using a novel, high-throughput method of respiration measurement that allows the measurement of individual embryonic and larval respiration rates, it was possible to make thousands of individual respiration measurements. In the first section, this method was used to measure respiration rates in the embryos and larvae of two polar echinoderms, the urchin Sterechinus neumayeri and the seastar Odontaster validus. Variation was examined in a variety of different larval cohorts as well as cohorts that were raised under different environmental conditions. This method was also applied to the poecilogenous spionid Streblospio benedicti an organism that produces two larval morphs—a plantotroph and a lecithotroph. Respiration measurements were made of both larval morphs at two different temperature regimes, 10°C and 22°C, and the rates were normalized to DNA content. Not only were respiration rates found to be higher in planktotrophs compared to lecithotrophs at both temperature treatments, but larvae raised at 22°C had significantly higher respiration rates than those raised at 10°C regardless of larval morphotype. These results of this thesis show the benefits of using a high throughput technique for measuring individual respiration rates to build stronger correlations regarding the degree of phenotypic variation that occurs within cohorts during early larval development. These results also demonstrate a presumably higher metabolic cost for a planktotrophic development program compared to a lecithotrophic development program even for different larvae morphs within the same species.