Mouse models were developed and evaluated to determine if potential health effects associated with intranasal and peroral exposure to microbial biotechnology agents could be detected. Mice were challenged with two dissimilar microorganisms: Pseudomonas aeruginosa AC869 and Escherichia coli BJ19. Intranasal challenge of mice with 1.7 × 108 CFU or 1.7 × 107 CFU of strain AC869 resulted in 100 per cent and 50 per cent mortality respectively. Peroral treatment with strain AC869 caused 33 per cent and 8 per cent mortality upon treatment with 2.2 × 109 and 2.2 × 108 CFU respectively. E. coli was not fatal after administration by either exposure route. Recovery of AC869 from lungs, small and large intestines and caecum following intranasal- and peroral-treatment was observed. E. coli BJ19 was recovered from the same four organs following peroral and intranasal challenge. Intranasal challenge resulted in a higher concentration and a longer persistence of strain BJ19 in the intestinal system than direct peroral challenge. In addition, increases in lung weights were associated with strains BJ19 and AC869 treatment. Translocation from the intestinal tract to the mesenteric lymph nodes (MLN), liver, and spleen and negative effects on tissue and body weights were detectable for both exposure routes and were dependent on the dosed strain. Overall, mice could be used to detect adverse health effects when dosed independently with microbial agents from different genera.