Gold nanoparticles (GNPs) of different sizes were used to carry out comparative fluorometric detection study on endotoxin. At excitation wavelength, 308 nm the GNPs exhibited strong emission intensity at wavelength 421 nm with varying intensities at 215.122, 234.965 and 262.551 for 15 nm (GNPs-I), 30 nm (GNPs-II) and 40 nm (GNPs-III), respectively. The different sizes of GNPs were interacted with endotoxin to study the effect of GNPs size on endotoxin detection. The electrostatic interaction between GNPs (GNPs-I, II, and III) and endotoxin led to the enhancement of the fluorescence intensities. The sensitivity of endotoxin detection was improved significantly by decreasing the size of the GNPs to 15 nm (GNPs-I). The endotoxin detection limit using GNPs-I was theoretically calculated to be 0.56×10−9 M using the formula 3SD/slope, and it was able to detect lower levels of endotoxin when compared to GNPs-II or GNPs-III. The GNPs-I showed excellent selectivity for endotoxin detection with the optimized pH and volumetric ratio. Most importantly the optimized size was successfully used to detect endotoxin in real samples (milk samples and fruit juices) with a recovery rate of 98–105%. © 2016 Elsevier B.V.