The flow cytometry system of the present invention includes a flow channel including an interrogation zone. A light source and a light detector are connected to the interrogation zone, such that a sample flowing through the interrogation zone can be optically analyzed through methods known in the art of flow cytometry. A bubble detector is connected to the flow channel. A controller is connected to the bubble detector and is adapted to perform a predetermined output in response to the detection of a bubble in the flow channel. The predetermined output may include alerting a user as to the presence of a bubble, flagging potentially corrupted data, and ceasing data collection until the interrogation zone is clear of bubbles.