The objective was to clarify the association between bulk tank milk somatic cell count (BTSCC) and total bacterial count (BTTBC) and coliform bacteria count (BTCBC) in a large set of data based on the currently accepted legal limit of BTSCC=400000/ml. We analysed the database obtained from one of four laboratories offering routine estimation of microbiological indicators and counts of somatic cells in bulk tank milk samples in the Czech Republic during the year 2003 (74174; 73921 and 33020 records of BTSCC, BTTBC and BTCBC estimations, respectively, in milk from 2769 suppliers). Raw data of BTSCC (with arithmetic mean 220000/ml; 95th percentile=502000/ml; 99th percentile=784000/ml) indicated that the BTSCC limit was exceeded in 12% of samples. BTSCC did not sufficiently reflect the hygiene status of particular producing herds because correlation coefficients between bulk tank milk somatic cell score (BTSCS) and log BTTBC or log BTCBC were low. Categorization of herds according to the percentage of records exceeding the BTSCC limit gave significantly higher correlation coefficients for the association between this characteristic and log BTTBC or log BTCBC (r=0·84 and r=0·68, respectively). The percentage of records exceeding the BTSCC limit was a useful tool to highlight problem herds kept in inadequate hygienic conditions in primary milk production. Likewise, the value of BTSCS>5 seemed to be a useful tool for the discrimination of problem herds.