In recent years, popularity of raw milk has increased in many industrialised countries. This study (i) enumerated total viable counts (TVC) and Escherichia coli counts, (ii) assessed prevalence of Staphylococcus (S.) aureus, Salmonella spp. and STEC, (iii) screened for methicillin resistant S. aureus (MRSA) and extended-spectrum β-lactamases (ESBL)-producing Enterobacteriaceae in sheep and goat tank milk samples collected throughout Switzerland and (iv) provided further strain characteristics on isolated pathogens and MRSA. One hundred and twenty-three tank milk samples from 116 farms were analysed. The median TVC was 3.8 log cfu mL−1. E. coli was detected in 16 (13.0%) and S. aureus in 18 (14.6%) samples. Polymerase chain reaction for stx genes was positive in 14 (11.4%) samples. MRSA were isolated from 4 (3.3%) samples. Salmonella spp. and ESBL-producing Enterobacteriaceae were not isolated.