Cyanobacterial bloom samples from the Gulf of Finland (northern Baltic Sea) were collected in July 2003 and analyzed for microcystins and nodularins, cyanobacterial peptide hepatotoxins, by ELISA, HPLC-UV and LC-MS. The blooms consisted mainly of the genera Nodularia, Anabaena and Aphanizomenon. The main hepatotoxin in the samples was nodularin-R (Nod-R), all the samples also contained demethylnodularin-R. The presence of microcystin-LR was confirmed in three locations out of nine by multiple reactant monitoring on the triple quadrupole mass spectrometer. This is the first reported finding of microcystins in the Baltic Sea from the open sea area. Anabaena was the likely producer of microcystin-LR in the samples.