A system and method for performing speckle correlation flow cytometry (SCFC). By subtracting out the stationary background when shining light through a sample (e.g., a vessel within a biological tissue), light only scattered by the desired targets (e.g., cells) can be captured and different types of targets (e.g., cells) can be distinguished by the autocorrelation of the speckle pattern. In this way, the targets (e.g., cells) can be classified and counted based on the features of their speckle correlations. The technique can be applied not only for noninvasive, label-free, in vivo CTC counting but also for counting other types of blood cells such as white blood cells or red blood cells.