With the advent of point-of-care diagnostics systems, investigation into properties of blood at micron scales is gaining fundamental importance. Past research has shown that blood displays significantly different properties at small scales than at conventional scales. This study investigates properties of blood flow in small non-circular passages (hydraulic diameter: 95-960 μm) under pulsatile condition. The observations are compared with flow of water under otherwise similar conditions. Prominent observation includes a more stable response to abrupt mass flow rate fluctuations as compared to water, which is attributed to the presence of deformable cells in blood. The study also reveals that, the pressure drop for blood flow with pulsations is less than for steady condition with the difference increasing with a reduction in microchannel size and flow rate. Such a comparative study facilitates development of models for blood flow at micro-scales, and will eventually aid in the design of future micro-Total Analysis Systems.