Mastitis is a multifactorial disease and the most costly dairy production issue. In spite of extensive literature on udder-health risk factors, effects of metabolic diseases, farmers’ competencies and livestock farming system on somatic cells count (SCC) are sparsely described. Herd-level or territorial-level factors affecting monthly composite milk weighted mean cow SCC (CMSCC) were analysed with a linear mixed effect model. The average CMSCC was 266000 cells/ml. Half of the herds had CMSCC >300000 cells/ml for 2–6 months a year, and 15% of herds for more than 7 months a year. CMSCC was positively associated with the number of cows, having a beef or fattening herd in addition to the dairy herd, the monthly average days in milk, the yearly age at first calving, the yearly proportion of purchased cows and the yearly culling rate. Moreover, a positive association is reported between CMSCC and the monthly proportion of cows probably with subacute ruminal acidosis (fat percentage minus protein percentage ⩽0·30%, for Holstein) and negative energy balance (protein to fat ratio ⩽0·66, for Holstein), the yearly average calving interval, having at least one dead cow and the mean monthly temperature. The association was negative for a predominant breed other than Holstein, the monthly milk production, the yearly dry-off period length, the monthly first calving cow proportion, having an autumn calving peak, being a Good Breeding Practices member, the monthly number of days with rain, the altitude and the territorial cattle density. CMSCC varied widely among the 11 dairy production areas. In conclusion, this study showed the average CMSCC for the French dairy cows, compared with international results. Moreover, it quantified the contribution of several factors to CMSCC, in particular metabolic diseases and the farm environment.