Abstract: A method and apparatus of multi-dye analysis of particles using flow cytometer. The method includes dying particles to be detected using two or more dyes; urging the particles through a capillary in a non-uniform flow; exciting a first of the particles within the capillary using a multiphoton excitation laser beam causing the two or more dyes each to fluoresce thereby producing a first output signal and a second output signal respectively; and detecting the first output signal and the second output signal. A second of the particles within the capillary being excited using the multiphoton excitation laser beam causing the two or more dyes each to fluoresce thereby producing a third output signal and a forth output signal respectively. The method finally includes comparing a ratio of the first output signal and the second output signal to a ratio of the third output signal and the forth output signal to detect a desired change in the particles.