Out of necessity, small bench top clinical diagnostic instruments have been limited in on-board features that can be packed into the dimensions of a stand-alone instrument. This often reduces the functionality of these machines to a narrow range of tests and can also substantially increase the complexity and cost of the consumable components. We have addressed these limitations in a novel bench top clinical device. With confocal optics in combination with an autofocusing method we are able to target and image a thin layer of cells for analysis of shape and spectral properties. Due to the non-CCD based detection method, the system has an optimized depth of focus that allows for detection of cells while rejecting bulk background fluorescence, thus greatly reducing background signal and increasing signal-to-noise. The flexibility in the cartridge design allows for a wide variety of assays, including multi- step reagent mixing and incubation, and multiple assays on a single sample. Further, use of volumetric capillaries allows the determination of absolute cell counts in specified volumes, eliminating the need for counting references. The multi-PMT detection takes advantage of assays using multiple stains. Bar code reading allows for sample identification and other information. On-board communications interfacing allows flexible LIS options, remote software upgrading, and detailed development and debug information access. We present laser-scanning cytometer with a small footprint that includes on-board liquid handling and facilitates a diverse set of clinical assays, while improving user-safety and ease of use.