A system is provided for spray coating medical devices, comprising a rotary atomizer with one or more rotary heads and a plurality of holders to hold a plurality of medical devices, such as stents, wherein the holders are positioned around a longitudinal axis of the rotary head. A method of using such a system is also provided. The invention enables the use of rotary atomizers to coat small medical devices with reduced waste of coating material and allows increased production throughput by the coating of multiple devices simultaneously. The rotary atomizer may be an electrostatic rotary atomizer. The holders and/or a holding structure on which the holders are mounted may move relative to the rotary atomizer.