Application of flow cytometry (FCM) to microbial analysis of milk is hampered by the presence of milk proteins and lipid particles. Here we report on the development of a rapid (less than or equal to 1-h) FCM assay based on enzymatic clearing of milk to determine total bacteria in milli. When bacteria were added to ultra-heat-treated milk, a good correlation (r greater than or equal to 0.98) between the FCM assay and the more conventional methods of plating and direct microscopic counting was achieved. Raw milk data showed a significant correlation (P < 0.01) and a good agreement (r = 0.91) between FCM and standard plate count methods. The detection limit of the FCM assay was less than or equal to 10(4) bacteria mi of milk(-1). This limit is below the level of detection required to satisfy legislation in many countries and states.