Abstract: Objectives: To evaluate thefeasibility of using automatic quantita-tive analysis of breath hold gatedmicro-CT images to detect and monitordisease in a mouse model of chronic pulmonary inflammation, and to com-pare image-based measurements with pulmonary function tests and histo-morphometry. Material and methods: Forty-nine A/J mice were used, divided into control and inflammation groups. Chronic inflammation was induced by silica aspiration. Fourteen animals wereimaged at baseline, and 4, 14, and 34 weeks after silica aspiration, using micro-CT synchronized with ventilator-induced breath holds. Lung input impedance was measured as well using forced oscillation techniques. Five additional animals from each group were killed after micro-CT for com-parison with histomorphometry. Results: At all time points, micro-CT measurements show statistically sig-nificant differences between the two groups, while first differences infunctional test parameters appear at 14 weeks. Micro-CT measurements correlate well with histomorphometry and discriminate diseased and healthy groups better than functional tests. Conclusion: Longitudinal studies using breath hold gated micro-CT are fea-sible on the silica-induced model of chronic pulmonary inflammation, and automatic measurements from micro-CT images correlate well with histo-morphometry, being more sensitive than functional tests to detect lung damage in this model.