This article explores the effect of horizontal and vertical setups on blend electrospinning with two polymers having vastly different properties - poly-ε-caprolactone and gelatin, and subsequent effect of the resulting microstructure on viability of seeded cells. Poly-ε-caprolactone and gelatin of varying blend concentrations were electrospun in horizontal and vertical setup orientations. NIH 3T3 fibroblasts were seeded on these scaffolds to assess cell viability changes in accordance with change in microstructure. Blend electrospinning yielded a heterogeneous microstructure in the vertical orientation beyond a critical concentration of gelatin, and a homogeneous microstructure in the horizontal orientation. Unblended poly-ε-caprolactone electrospinning showed no significant difference in fibre diameter or pore size in either orientation. Mechanical testing showed reduced elasticity when poly-ε-caprolactone is blended with gelatin but an overall increase in tensile strength in the vertically spun samples. Cells on vertically spun samples showed significantly higher viabilities by day 7. The composite microstructure obtained in vertically spun poly-ε-caprolactone -gelatin blends has a positive effect on viability of seeded cells. Such scaffolds can be considered suitable candidates for cardiovascular tissue engineering where cell infiltration is crucial.