Optical methods are widely used in biophotonic applications. They can be used for imaging cellular structures and living tissues. They also provide a tool to analyse cell cultures and cell suspensions. For example fluorescence, optical absorption or optical scattering can account for the contrast mechanism. Luminescence has also found various application areas. Luminescence from modified gene reporters can be measured to quantify biological phenomena and dynamic processes. In this paper the principles of phase sensitive detection and photon counting instrumentation systems to detect low-intensity light are shortly reviewed. They are typically using a photomultiplier tube as a detecting element. We discuss the experimental approach and the potential application areas in the context of elastic light scattering measurements of single particles and cells as well as in characterization of tissue-mimicking phantoms. Moreover, we describe a photon counting measurement system for measuring luminescence and show some results of monitoring luminescence in supernatant samples from cell cultures. The same instrument is capable to measure elastic light scattering from single cells and tissue-mimicking phantoms by using a phase sensitive detection with small modifications..