In this study, gliotoxin production by Aspergillus fumigatus strains from animal environment is studied. Moreover, a rapid, easy and environment-friendly micro-analytical sample treatment procedure coupled with LC-MS/MS was applied for the determination of gliotoxin from A. fumigatus cultures. The ability of gliotoxin production by 143 strains was assayed in yeast extract sucrose agar, and 1 ml of chloroform was used for toxin extraction without further clean-up. Mean recoveries at two spiking levels (2500 and 7000 ng/g; n = 6) were 100.3 ± 6.6 % relative SD (RSD) and 92.4 ± 3.8 % RSD. Repeatability and within-laboratory reproducibility for different concentration levels of gliotoxin (25 to 1000 ng/ml; n = 12) ranged from 0.3 to 5.4 % RSD and from 3.9 to 12.7 % RSD, respectively. The detection limit of the analytical method was 3.5 ng/g. The ability for gliotoxin production by A. fumigatus revealed that 61.5 % of the strains were able to produce the toxin at levels ranging from LOQ to 3430.5 ng/g. However, all the tested samples had similar percentages of producing strains (81.8 to 86.6 %). The micro-analytical sample treatment coupled with LC-MS/MS detection is a precise and useful methodology for determining gliotoxin from fungal extracts of A. fumigatus and allows working both fast and safely and also reducing the effect on the environment. This toxin plays a critical role in the pathobiology of A. fumigatus, and its presence in animal environments could affect animal health and productivity; in addition, there are risks of contamination for rural workers during handling and storage of animal feedstuffs.