The objective of this study was to examine the quarter health status of quarter-individually and conventionally milked cows. The MultiLactor®, a quarter-individual milking system (MULTI), has single guided tubes which provide milking on the quarter level with a low system vacuum level (37 kPa), sequential pulsation and periodic air inlet. The conventional milking system (CON) was equipped with a milking cluster where the system vacuum level was adjusted to 40 kPa. A total of 84 German Holstein cows, randomly divided into two groups, were included in the study. Over a period of 32 trial weeks, quarter foremilk samples were taken every week to determine somatic cell count (SCC). Bacteriological examinations and udder palpation were conducted at three different times. During the trial period, median SCC of quarter foremilk samples in both groups did not exceed the threshold value of 100,000 cells/ml. The results of the F test showed that the milking system (P = 0.0587) and days in milk (DIM) (P = 0.8066) had no significant effects on the quarter health status. On the other hand, lactation (P = 0.0396), quarter health status in the previous week (P < 0.0001) and trial week (P = 0.0061) affected quarter health status significantly. The estimated probabilities of the occurrence of a suspicious quarter (SCC > 100,000 cells/ml) were 19.97% (CON) and 31.72% (MULTI). However, the test of differences in the Least Square Means (LSM) showed no significant differences (P = 0.0585) between CON and MULTI. The estimated probability of quarters becoming suspicious during the first lactation was 12.51% for both groups. With an increasing number of lactation, the probability of a quarter becoming suspicious clearly increased (2nd lactation: 32.73% and 3rd lactation: 36.19%). The results also showed that the percentage of quarters with bacteriological findings revealed a stronger increase over time for MULTI than for CON.