The present invention pertains to a portable apparatus for quantitatively measuring the concentration of specific substances in test samples of a lateral flow or microplate assay in medical, biomedical and chemical applications, and for making subsequent analysis and diagnosis. The portable apparatus includes a sample tray for carrying and aligning the test sample in the apparatus; a enclosure that may also serves as the frame of the apparatus; a digital image acquisition system that is used to obtain the digital image of the test sample on the sample tray; and a data display, processing, and analysis unit that is a general purpose or dedicated computer, such as a handheld computer (HHC), a pocket personal computer (PPC), a personal digital assistant (PDA), a palm-top computer, a laptop computer, or a dedicated microprocessor and associated hardware, for measuring the concentration of specific substances in the test sample, and making subsequent analysis and diagnosis, based on the measurement, statistical data, prior knowledge and mathematical model. The stated enclosure and frame, the digital image acquisition system, and the data display, processing and analysis unit are integrated to form the portable apparatus for various applications. The integrated apparatus of this invention, with a possible name—Portable Intelligent Multi-Diagnoser (PIMD), thus forms a portable and multiple-purpose tool for measuring the concentration of specific substances in test samples, and making subsequent analysis and diagnosis in a variety of settings, such as a mobile site, point of care or near patient care, and small laboratories.