To determine regional pulmonary microvascular mean transit times (MTTs), we used electrocardiogram-gated X-ray computed tomographic imaging to follow bolus radiopaque contrast material through the lungs in anesthetized animals (7 dogs and 1 pig, prone and supine). By deconvolution/reconvolution of regional time-attenuation curves obtained from parenchyma and large lobar arteries, we estimated the microvascular residue function and reconstituted the regional microvascular time-attenuation curves and, thus, regional microvascular MTTs. The mean microvascular MTTs in the supine and prone postures were 3.94 ± 1.0 and 3.40 ± 0.84 (mean ± SD), respectively. The dependent-nondependent vertical gradient of MTT was greater in the supine [slope = 0.25 ± 0.10 (SD), P < 0.001 by t-test] than in the prone (−0.03 ± 0.06 in 6 of 8 animals; 2 outliers had positive slopes) posture. In both postures, there was a trend toward faster transit times in the dorsal-basal lung region in six of the eight animals, suggesting gravity-independent higher vascular conductance dorsocaudally. We conclude that deconvolution methods, in association with electrocardiogram-gated high-speed X-ray computed tomography, can provide insights into regional heterogeneity of pulmonary microvascular MTT in vivo.