A centrifuge system with an externally positioned sensor assembly for detecting the separation of components in a fluid sample, such as platelets in a blood sample. The system includes a centrifuge with a drive portion and a rotor portion with a sample reservoir or centrifuge bag for receiving and containing a fluid sample during rotation of the rotor portion. An external sensor assembly is positioned relative to the centrifuge to direct a radiation beam from a radiation source through the rotor portion and the centrifuge bag and to allow a detector to receive the lower-intensity radiation beams at a location external to the rotor portion. In one embodiment, the rotor portion is fabricated from a transparent material and extends radially outward from the sides of the drive portion to allow the radiation source and detector to be positioned externally on opposing sides of the extending rotor portion.