Two types of commercially available ELISA kits for the immunoassay of cyanobacterial microcystins were evaluated for potential interference effects due to methanol, salinity, pH, plasticware and cyanobacterial extract. Of the treatments examined, methanol had the greatest effect, giving false positive microcystin concentrations with increasing methanol concentrations up to 30% (v/v) compared with the negative calibrators of each kit. False positive microcystin results were also produced with increasing salinity up to full strength seawater. Decreases in microcystin-LR equivalents were observed when assaying purified microcystin-LR at pH values between 6.25 and 10. Aqueous microcystin-LR solutions in plastic microcentrifuge tubes after pipetting with disposable plastic tips had lower toxin concentrations than expected when analysed by ELISA. Indicated microcystin concentrations in cyanobacterial extracts varied between kit types and the choice of blanks used. Although ELISAs can be useful tools for the screening of water and cyanobacterial blooms for microcystins and nodularins, users should be aware that commercial kits can be susceptible to interference by commonly encountered environmental and laboratory conditions and materials.