An experimental study was conducted to investigate the potential use of intravascular gene therapy with adenovirus-mediated (Ad) vascular endothelial growth factor (VEGF) or angiopoietin-1 (Ang-1) for the enhancement of muscle flap perfusion and to evaluate the effect of therapy on microcirculatory hemodynamics and microvascular permeability in vivo by using a cremaster muscle flap model in the rat. The cremaster tube flap was left intact after isolation of the pudo-epigastric pedicle. A total of 90 male Sprague-Dawley rats were divided into five groups of 18 each, according to the type of intraarterial treatment. Control flaps received phosphate-buffered saline. Group 2 (the control gene encoding green fluorescent protein, Ad-GFP) served as the adenovirus control. In Groups 3, 4, and 5, flaps were pretreated with Ad-VEGF, Ad-Ang-1, and Ad-Ang-1 + Ad-VEGF, respectively. Flaps were preserved in a subcutaneous pocket in the hindlimb for evaluation of functional capillary density and microvascular permeability indices at 3, 7, and 14 days by intravital microscopy system. At day 7 and 14, Ad-VEGF, Ad-Ang-1, and combined treatment groups showed significantly higher numbers of capillary densities when compared with control and Ad-GFP groups (p < 0.05). At day 14, Ad-VEGF was the superior treatment group compared with Ad-Ang-1 and Ad-VEGF + Ad-Ang-1 (p < 0.05). Overall, there was a linear increase in the number of functional capillaries in all treatment groups (p < 0.05). At day 3 after Ad-Ang-1 therapy, a significantly lower permeability index was found when compared with Ad-VEGF + Ad-Ang-1 and Ad-VEGF alone treatment (p < 0.05). At day 7, the Ad-VEGF group had the highest score of permeability index compared with control, combined, and Ad-Ang-1 groups (p < 0.05). Histologic evaluation of muscle flaps demonstrated mild focal inflammation. There was evidence of mild vasculitis in all flaps except control muscles. Intravascular angiogenic therapy with Ad-VEGF or Ad-Ang-1 was technically feasible, as demonstrated by expression of the control gene, GFP, along the vascular tree. All treatment groups increased perfusion of the muscle flap over a period of 14 days, indicating a long-lasting effect of gene therapy. Ang-1 alone or in combination with VEGF was as effective as VEGF alone in augmenting muscle perfusion with more stable vessels 1 week after gene therapy.