The Auditorium space has superb acoustics thanks to the wooden baffles in the ceiling. Enhancing the room's beauty and connection to science is the decorative, computer-generated image of a DNA molecule displayed in the dark blue frieze along the top of the wall.

The 360-seat auditorium is the site of meetings that scientists from around the world attend each year. It is also the venue for the CSHL Cultural Series of concerts and lectures open to the public. This is home to the department that organizes the CSHL Meetings and Courses Program, which brings over 8,000 scientists to CSHL every year. CSHL proudly presented American pianist Matthew Graybill in April 2019.