The recent availability of a high-throughput milk analyzer performing a partial differential somatic cell count (DSCC) opened new opportunities in investigations on bovine udder health. This analyzer has a potential limitation on the accuracy of measurements when the somatic cell count (SCC) is below 50,000 cells/mL, values characterizing a good proportion of lactating cows in many herds. We obtained data for cows below this threshold, assessed the repeatability of these measurements and investigated the relationship between DSCC and udder health, milk composition and yield. Overall, 3022 cow milk test records performed on a Fossomatic™ 7/DC (Foss A/S, Hillerød, Denmark) were considered; 901 of them had an SCC ≤ 50,000 cells/mL. These latter samples were analyzed by qPCR to identify the presence of bacteria. Overall, 20.75% of the samples (187) were positive. However, the health status did not have any significant association with DSCC. The analysis of the association of DSCC on milk fat, protein and casein showed a significant decrease in their proportions as the DSCC increased, whereas it was not observed for milk yield and lactose. Therefore, DSCC in very low SCC cows may be suggested as a marker to identify early changes in milk composition.