Particle analyzers having scintillation counters are provided. Particle analyzers of interest include a flow cell for transporting particles in a flow stream, a light source for irradiating a particle in the flow stream at an interrogation point, a particle-modulated light detector for detecting light from the interrogation point, and a scintillation counter for assessing particle radioactivity. In embodiments, the scintillation counter is positioned within the flow cell and configured generate particle radioactivity data that may be associated with a given particle in a plurality of particles. Methods and non-transitory computer readable storage media for practicing the invention are also provided.