AbstractThe maximum length of DNA molecules that can be separated by gel electrophoresis can be increased greatly by periodically altering the direction of the electric field with respect to the gel by an angle that exceeds 90°. One method involves rotating the gel by the desired angle in alternate directions periodically during electrophoresis. We describe a modification of the rotating gel electrophoresis apparatus developed by Serwer (Electrophoresis1987, 8, 301–304) that uses a pneumatic rotary actuator instead of a stepping motor, hence reducing the cost by about 50 %. Other advantages of our design are a lower center of gravity that makes the apparatus more stable and the removal of all electrical power from beneath the fluid‐filled electrophoresis chamber. We present data demonstrating the separation of chromosomal length DNA molecules fromSaccharomyces cerevisiaestrain 334 into 14 resolved bands in parallel l