Microarrays of lipids containing gangliosides were fabricated on surfaces coated with gamma-aminopropylsilane. A fluorescence microarray scanner was used to detect the binding of toxins to these arrays. The specific binding of cholera and tetanus toxins to microspots containing GM1 and GT1b gangliosides, respectively, was demonstrated. These results suggest the possibility of using ganglioside microarrays for multiplexed toxin detection and the screening of compounds that can inhibit toxin binding.