Nucleic acid analysis has provided useful tools to study recent growth and mortality of young fishes and their responses to environmental variability. The ratio of RNA-DNA (R/D) has been shown to respond to changes in feeding conditions and growth after periods as short as 1-3 days in a variety of fish species. The earliest studies used primarily UV-based methods, but most investigators now use more sensitive, fluorometric dye-binding assays to estimate RNA and DNA in individual larvae. These newer methods are very sensitive to procedural details and choice of standards. Analytical methods, normalization and calibration procedures to optimize information obtained from nucleic acid analysis are discussed. We present examples illustrating the technique's utility, and problems encountered when applying nucleic acid-based indices to fish larvae and early juveniles. The wide use of R/D analysis in studies of fish early life stages, together with a proliferation of analytical methods, demands a major intercalibration exercise.