The cyanobacterial hepatotoxic alkaloid cylindrospermopsin (CYL) is of increased concern to public health due to the spreading of its main producer, Cylindrospermopsis raciborskii, around the globe. Here we present results of an evaluation of the possibility to analyse environmental samples for their content of CYL based on HPLC with photo diode array detection as an alternative to costly LC-MS approaches. A gradient from 0% to 50% aqueous methanol (+0.05% trifluoroacetic acid) in 20 min proved to be highly reproducible with respect to peak height, peak area, and retention time of purified CYL. Good linearity of peak area response was found for 1-300 ng CYL on column. For a good performance the duration of equilibration prior to individual runs was crucial. Extraction from cell material (culture and bloom) was efficiently done with pure water in one extraction step and CYL contents determined matched well with results previously obtained by LC-MS. When different seston matrices were added to cultured cells to mimic realistic environmental samples, however, peaks eluting close to CYL in chromatograms restrained the performance. The data presented show a limitation of HPLC-PDA analysis for trace amounts of CYL in environmental samples but also underline the potential of an inexpensive and fast analysis for various purposes.