Diatoms in the Southern Ocean are limited by iron and light, and therefore produce little biomass. Sufficient biomass for analysis under these conditions requires large sample volumes, and diatom samples are therefore often pre-concentrated on a filter. A method for the digestion of diatom cells on polycarbonate filters, that is also suitable for trace metal analysis, is described here. Additional analysis by inductively coupled plasma-optical emission spectroscopy (ICP-OES) is used for the determination of biogenic silicon. Although several procedures were tested, the method of Hauptkorn et al., which uses tetramethylammonium hydroxide for the destruction of silicon is adapted here [Hauptkorn et al. (2001) Fres J Anal Chem 370:246–250]. Additional nitric acid is added to destroy the polycarbonate filters. The described method results in clear digests and a good correlation between cell numbers and silicon content. Using this procedure, the cellular silicon content for Chaetoceros brevis was determined as 86 ± 4 fmol cell−1. For Thalassiosira sp. a sensitivity effect was observed, and silicon content was determined as $$ Si{\text{ = 4}}{\text{.2x10}}^{{{\text{ - 7}}}} {\left( {{\text{1 - exp}}^{{{\text{ - 2}}{\text{.2x10}}^{{{\text{ - 7}}}} {\text{cells}}}} } \right)} $$ . The obtained cellular silicon contents are in good agreement with values presented in the literature.