Quality control and quality assurance are essential requirements of modern flow cytometric analysis. These aspects are important not only from the point of view of scientific rigour but also from a regulatory perspective. In light of this, we sought to implement a means of tracking instrument performance on a BD Influx flow cytometer that has no manufacturer supplied software for this purpose. Our approach was based on the widely utilized values of Qr (relative fluorescence detection efficiency) and Br (relative optical background fluorescence) that are a modification of those originally proposed by Hoffman and Chase(1). We present example results of our software, ConFlux, with those obtained using BD Biosciences Cytometer Setup and Tracking application on cuvette based flow cytometers. Of particular interest is the impact of manual daily alignment by skilled operators on the adjustments that the ConFlux software needs to make to reach previously defined target values. We compared these results with those obtained using cuvette based systems featuring fixed alignment and gel-coupled optics from both BD FACSAria and BD LSRII cytometers.