Background. More than 4,000 cases of acute disease in humans were reported during the mass Q fever outbreak in the Netherlands in 2007–2010. The Coxiella burnetii NL3262 strain was isolated during this outbreak from an aborted placenta of a goat and was studied using means of molecular biology and bioinformation techniques. Goals. Approbation of a new bioinformatics approach – formal order analysis – to study the origin of the strains that caused a massive outbreak of Q fever in the Netherlands using the C. burnetii NL3262 strain. Methodology. New tools of the formal order analysis (FOA) «Map of Genes» and «Matrix of Similarity» (available at http://foarlab. org) were used in this work to study the degree of similarity of the genome (chromosome, plasmid) of this strain with the genomes of other strains of C. burnetii. The nucleotide sequences of the chromosomes of 10 C. burnetii strains and 8 plasmids were loaded from GenBank: www.ncbi.nlm.nih.gov/genome. Results. The map of genes data showed that the chromosome of NL3262 strain significantly distanced from the chromosome of other strains by the characteristic of the average remoteness of nucleotides in the chromosome (g) that ranged from 1.448295 (for Dugway 5J108-111) to 1.448865 1.449640 (for CbRSA331). This may be due to the presence of 106 copies of the «transposase family IS110» gene associated with the growth of virulence, while in the chromosomes of other strains their number ranged only from 1 to 48. The similarity matrix showed that 84.9% of C. burnetii NL3262 chromosome components had complete (100%) homology with chromosome components of strain Z3055. The percentage of similar components ranged from 12.06 to 47.14 for chromosomes of other strains. Plasmids of the pQpH1 type of strains NL3262 and RSA 331 contained 50.0% of components with complete homology. For the same type of plasmids of strain RSA 493 and its clones, the index varied from 28.89 to 29.89%, and for plasmids of other types it was from 5.56 to 6.74%. It is shown that the chromosomes of ...