The study aim was to determine the best inoculation route for virulotyping Enterococcus cecorum in a chicken embryo lethality assay (ELA). Twenty-eight genetically different strains were used. Fourteen strains were isolated from cloaca swabs of broiler reproduction chickens (cloaca strains) and 14 strains from broilers with E. cecorum lesions (lesion strains). In all ELAs, 12-day incubated embryonated broiler eggs were inoculated with approximately 100 colony-forming units of E. cecorum/egg. Twenty embryos per inoculation route and strain were used in each of three experiments. In Experiment 1, four cloaca and four lesion strains were inoculated via various routes, i.e. albumen, amniotic cavity, allantoic cavity, chorioallantoic membrane, intravenous or air chamber. The albumen inoculation route showed low mortality with cloaca strains, high mortality with lesion strains and the largest difference in mortality between these groups of strains (≥60%). This route was therefore used in subsequent experiments. In Experiment 2, the same strains were used to test reproducibility, which proved to be generally good. All 28 strains were thereafter used in Experiment 3. In the three experiments, mortality caused by cloaca and lesion strains ranged from 0-25% and from 15-100%, respectively. Recovery rates, assessed in all experiments after albumen inoculation, were significantly lower from eggs inoculated with cloaca strains, compared to lesion strain-inoculated eggs (P < 0.05). However, the bacterial load of eggs with positive recovery was similar in both groups. In conclusion, the albumen inoculation route appeared to be the best to virulotype E. cecorum strains.RESEARCH HIGHLIGHTS The albumen route is the best to differentiate between E. cecorum strains.Egg albumen likely affects cloaca E. cecorum strains more than lesion strains.Based on SNPs, E. cecorum cloaca strains are clustered as well as lesions strains.