Objectives were to investigate somatic cell counts (SCC) and total bacterial counts (TBC) in the raw bulk-tank milk of sheep flocks in Greece, to study factors potentially influencing increased SCC and TBC in the bulk-tank milk of sheep and to evaluate possible associations of SCC and TBC with milk content. Throughout Greece, 325 dairy sheep flocks were visited for collection of milk sampling for somatic cell counting, microbiological examination and composition measurement. Geometric mean SCC were 0.488 × 106 cells mL−1; geometric mean TBC were 398 × 103 cfu mL−1; 228 staphylococcal isolates were recovered form 206 flocks (63.4%). Multivariable analyses revealed annual incidence risk of clinical mastitis, age of the farmer and month into lactation period (among 53 variables) to be significant for SCC > 1.0 × 106 cells mL−1 and month into lactation period at sampling and availability of mechanical ventilators (among 58 variables) to be significant for TBC > 1500 × 103 cfu mL−1. Negative correlation of SCC with fat, total protein and lactose and positive correlation of SCC with added water were found. With SCC > 1.0 × 106 cells mL−1, significant reduction of protein content (2%) was observed, whilst in flocks with SCC > 1.5 × 106 cells mL−1, significantly lower annual milk production per ewe (42.9%) was recorded.