Intracellular contents of carbon, nitrogen and phosphorus in phytoplankton cells are traditionally measured using concentrates containing thousands to millions of cells. In this study we have used a Nuclear MicroProbe (NMP) as an approach for the determination of C, N and P concentrations in single filaments of three cyanobacteria species: Anabaena sp., Nodularia spumigena and Aphanizomenon flos-aquae var. klebahnii isolated from Baltic Sea water. Estimations of C, N and P content per cell have been calculated and compared with the concentrations found with traditional bulk methods. No significant differences regarding the C, N and P cellular content were found between the two methods for each of the species tested (p < 0.05). From our results we conclude that the use of NMP can be a useful tool for studying the elemental contents in single phytoplankton cells