Clinical microscopy is a versatile and robust tool used for the diagnosis of a plethora of diseases. However, due to various reasons, it remains inaccessible in resource limited settings. In this article, we present an automated and costeffective alternative to microscopy for use in clinical diagnostics. With the use of custom optics and microfluidics, we demonstrate a field-portable imaging flow cytometry system. Using the presented system, we have been able to image 586 cells per second. We demonstrate the clinical relevance of the proposed system by differentiating between suspensions of healthy and sphered RBCs based on high-throughput morphometric analysis. The instrument presented here is a major advancement in the domain of field portable diagnostics as it enables fast and robust quantitative diagnostic testing at the point-of-care.