Abstract: Effective management of Baltic clupeids, which are valuable commercially and ecologically, requires the biomass control. The acoustical techniques are recognized as effective in fish stock assessment. The study of Baltic herring and sprat individual backscattering characteristics is required for the accurate biomass estimation using acoustical techniques. The previous measurements demonstrated significant dependence of the backscattering properties of Baltic clupeids on their geographical location. For southern Baltic Sea the properties are not recognized sufficiently yet. Accounting for that fish swimbladder morphometry effectively impacts on the backscattering, it is important to study the morphometry of southern Baltic herring and sprat. It motivated the paper study. The paper is addressed to the development of the methodology of the analysis of the accurate shape of the swimbladder. The way of the fish catch, transport and storage, the X-ray irradiation and the X-ray image analysis was developed.