A photopheresis system (200) is disclosed, and that may be configured to execute one or more protocols for collecting buffy coat from blood processed by the photopheresis system (200). The photopheresis system (200) includes a centrifuge (210) which rotates to separate blood into a plasma layer (322), a buffy coat layer (320), and a red blood cell layer (318). A location of an interface between said buffy coat layer and said red blood cell layer is monitored in a first monitoring step. An existence of a first condition and a second condition is monitored in a second monitoring step. Fluid including buffy coat from the buffy coat layer (320) is directed out of a port (222) of the centrifuge (210) and into a first container (270, 280) in response to an identification of the existence of the first condition or the second condition.
