Most of the physiological fluids are transported through peristalsis of the walls which is the inherent neuromuscular property of tube smooth muscle structure. The present paper deals with the transport of seminal fluid introducing the microstructural effects and peripheral-layer viscosity effects on the flow rate and the drag for the system. It has been observed that the flow rate increases tremendously with the decrease of the peripheral layer viscosity whereas a reverse trend has been noted for the frictional drag. Further other sub-structural effects i.e. the effects of relative rotational viscosity and viscosity gradients have also been broughtout and discussed.