The East African Rift Valley Lakes Bogoria and Nakuru sometimes host around 75% of the world population of lesser flamingos Phoeniconaias minor. In this area, mysterious flamingo die-offs have occupied researchers for four decades. Recently, cyanobacterial toxins came into the fore as a possible explanation for mass mortalities because the main food source of lesser flamingos is the cyanobacterium Arthrospira fusiformis. We took weekly samples from July 2008 to November 2009 from Lakes Nakuru and Bogoria and analyzed them by high performance liquid chromatography for microcystins. Monthly, samples were cross-checked using protein phosphatase inhibition assays with lower detection limits and additionally screened for polar toxins. During our study period, three flamingo die-offs occurred at L. Bogoria and we were able to analyze tissues of 20 carcasses collected at the shoreline. No cyanotoxins were detected either in plankton samples or in flamingo tissues. Accordingly, other reasons such as food composition or bird diseases played a key role in the observed flamingo die-offs.