This study describes the performance of a new waveguide flow cell constructed from Teflon AF 1 (TFC) and the potential use of fiber optic splitters to replace collection objectives and dichroic mirrors. The TFC has the unique optical property that the refractive index of the polymer is lower than water and therefore, water filled TFC behaves and functions as a liquid core waveguide. Thus, as cells flow through the TFC and are illuminated by a laser orthogonal to the flow direction, scattered and fluorescent light is directed down the axis of the TFC to a fiber optic. The total signal in the fiber optic is then split into multiple fibers by fiber optic splitters to enable measurement of signal intensities at different wavelengths. Optical filters are placed at the terminus of each fiber before measurement of specific wavelengths by a PMT. The constructed system was used to measure DNA content of CHO and yeast cells. Polystyrene beads were used for alignment and to assess the performance of the system. Polystyrene beads were observed to produce light scattering signals with unique bimodal characteristics dependent on the direction of flow relative to the collecting fiber optic. (1) and have since been refined into highly developed, sophisticated instruments. Over this time, the basic principles have not been changed significantly. In traditional flow cytometry, the illuminating laser beam and the light collection optics are placed in the same plane perpendicular to the flow stream. In most current instrument configurations microscope objectives gather scattered or fluorescent light. In place of microscope objectives, optical waveguides butted against the flow cell wall have been proposed and shown to collect light similar to microscope objectives (2). The collected light is then passed through a series of dichroic mirrors and bandpass filters to measure light from fluorophores correlated with a specific aspect of cell physiology. For high accuracy and precision, this traditional arrangement requires a precise alignment between the illumination optics, the flow stream, the collection optics, and the dichroic mirrors and filters used. Properly aligning these elements is a sensitive task that requires considerable skill and experience.Current research to expand this technology has taken two directions: (i) development of higher-end cytometers with increasing signal strength, numbers of illuminating lasers, and fluorescence parameters analyzed (3-5) and (ii) development of instruments that are smaller, less expensive, and more accessible (Guava Technologies, Accuri) (6-8). This report describes an alternate configuration that has the potential to make cytometers less expensive, more accessible, and more robust.The described instrument configuration uses a Teflon AF capillary as the flow cell (TFC). The TFC has the unique optical property that the refractive index of the polymer (n 5 1.290) is lower than water (n 5 1.333) (9). Thus, a water filled TFC