As condition is a key variable in population dynamics (especially for survival, growth and reproduction), the use of well-defined and accurate fish condition indices is capital. In particular, condition indices (morphometric, bioenergetic and biochemical) have never been compared and validated for the European anchovy Engraulis encrasicolus, the European pilchard Sardina pilchardus and the European sprat Sprattus sprattus. The accuracy of two indirect methods, the morphometric relative condition index Kn and the bioenergetics index determined with the Distell Fish Fatmeter was investigated by comparing with a direct measure of relative lipid content carried out with a thin layer chromatography-flame ionization detector. Estimations from the fatmeter correlated quite well with the relative lipid contents of all species, regardless of the reproductive period (R2 = 0.69 for anchovy, R2 = 0.75 for sprat and R2 = 0.48 for sardine). Kn correlated more poorly with relative lipid content (R2 = 0.22 for anchovy and R2 = 0.41 for sardine, ns for sprat), especially during the reproductive period, pointing out the difficulty for such an index to precisely reflect changes in fat allocation. During the reproductive period, changes in Kn could reflect other processes, such as changes in protein content. Therefore, these different types of commonly used indices do not reflect exactly the same type of energy stores. The high repeatability of the fatmeter was brought to light, so that only one measurement on each fish side may be necessary to evaluate the relative lipid content of a small pelagic fish. Finally, fatmeter measurements were not affected by freezing storage up to one month for anchovy (R2 = 0.66) and sardine (R2 = 0.90), making it possible to use frozen samples of both commercial and scientific survey. In contrast, the freezing storage for sprat should be avoided. Based on this study, the Fatmeter appears to be a suitable indirect method to assess condition and fat content of sardine and anchovy on a large number of individuals.