Walleye pollock are an important component of the eastern Bering Sea ecosystem due to their vast numbers and biomass and are of great commercial importance. Their recruitment in the eastern Bering Sea is not well understood but it is largely determined during the first year, so the larval stage may play a significant role. Starvation may contribute to the high and variable mortality that occurs during the larval stage so it is important to monitor and quantify it. This metadata describes data from laboratory and field studies conducted from 2009 to 2012 for NPRB project 926. The project completed the development of an assay using flow cytometric cell cycle analysis to assess the physiological condition of walleye pollock larvae, and applied it to field collected specimens. The use of RNA to improve the accuracy of the assay was also investigated, as well as the relationship between flow cytometric measurements and growth. Results showed that the overall classification accuracy of the assay (healthy or unhealthy) ranged between 75 and 83% depending on the type of cross-validation testing. A nuclear RNA variable (the ratio of the number of S phase nuclei to the number of high nuclear RNA content G1 phase nuclei) improved overall classification accuracy by 11% compared to a model without it. Unhealthy walleye pollock larvae were present in the southeastern Bering Sea in 2009, and this was most likely the result of cold environmental conditions affecting prey availability and larval feeding. In 2010, no unhealthy larvae were detected. This may be the result of less spatial coverage and smaller collections of larvae than in 2009, given that the environmental conditions were similar between years.