Lipid class dynamics, the pattern of change in the primary form and location of lipid stores and their relationship with standard length (LS), were investigated in collections of young-of-the-year weakfish Cynoscion regalis for the purpose of determining the utility of this analysis as an indication of condition. The separation of total lipids into individual classes and the analysis of potential storage depots revealed the general patterns of lipid class dynamics and energy storage in C. regalis during their period of juvenile estuarine residency. Phospholipid and cholesterol exhibited moderate but variable (8·1–40·0 and 1·3–21·5 mg g−1, respectively) concentrations across the entire juvenile period and were the predominant lipid classes in juveniles <100 mm LS, while wax ester concentrations were low (c. 1 mg g−1) and exhibited the least amount of variability among lipid classes. Triacylglycerols (TAG) and free fatty acids (FFA) exhibited similar dynamics, with relatively low concentrations (<15 mg g−1) in individuals ≤100 mm LS. In larger juveniles both TAG and FFA concentrations generally increased rapidly, though there was considerable variability in both measures (0·0–199·7 and 0·0–49·7 mg g−1, respectively). Increasing levels of lipids, primarily in the form of TAG, with size indicated an accumulation of energy reserves with growth, thus providing an indication of individual condition for larger juveniles. Separate analysis of liver, viscera and the remaining carcass indicated that liver and viscera did not represent a significant depot of TAG reserves. Analysis of samples derived from whole juvenile C. regalis thus provided an accurate estimate of energy reserves.