During HTST heating of milk, some thermoduric bacteria, as well as bacterial spores, can survive. Such microbes can attach and form biofilms downstream from the heating section. During long run periods, some portions of the regeneration and cooling sections will be at a temperature that will permit spore germination and bacterial growth. This can have a detrimental effect on product quality as bacterial numbers in the biofilm increases, and bacteria and biofilm material are released into the milk. Our aim was to determine when increased bacterial load occurs during such long operation times. A lab-scale heat exchanger was fabricated consisting of heating and cooling sections, peristaltic pumps, with temperature recorded on inlet and outlet positions on the product and heating and cooling water. Raw milk was run in a single pass through the heat exchanger for 18 h on 5 separate occasions. Samples were collected every other hour in the first 6 h and then every hour for the remaining hours. Total plate counts of bacteria present in each sample were enumerated using standard methods agar incubated aerobically at 30°C for 48 h. In general, the bacterial counts remained at the baseline level (<10² cfu/mL) for the first 10 to 12 h. As the processing continued there was an increase in bacterial numbers. There was a fluctuation in bacterial numbers throughout the 18 h of operation, especially after 10 h when hourly measurements fluctuated between 10³ and 10¹ cfu/mL. The fluctuations in bacterial numbers were attributed to biofilm material with associated bacteria being released from the heat exchanger plates on an intermittent basis. In conclusion, running a pasteurizer for extended times will lead to increased bacterial load in pasteurized milk which can lower product quality and cause contamination of any downstream processing systems. Further work is being performed on identifying the bacteria that were being released into milk and in which part of the cooling heat exchanging they are growing.