The objectives of this work were (a) to describe the incidence risk of subclinical mastitis in dairy flocks throughout the milking period, (b) to present potential associations of subclinical mastitis with the quality of milk and (c) to identify risk factors for high-incidence risk of the infection. A longitudinal study was performed in 12 dairy sheep flocks in Greece. Mammary secretion samples from 240 ewes and bulk-tank milk samples were collected in four repeated visits over a period of six months for bacteriological, chemical and cytological examinations. Overall, the incidence risk of subclinical mastitis throughout the study period was 51.7%, and it varied among farms from 25.0% to 75.0%. The respective figure for staphylococcal subclinical mastitis was 48.8%. The incidence risk of recurrence of subclinical mastitis among ewes in the flocks was 35.4%. The most frequently identified bacteria from cases of subclinical mastitis were and ; of the mastitis-causing staphylococcal isolates, 65.4% were biofilm-forming. Somatic cell counts in bulk-tank milk progressively increased as the lactation period advanced, with significant increases seen on the third and fourth visits to the farms. Somatic cell counts in bulk-tank milk correlated well with prevalence of subclinical mastitis in flocks. A significant inverse correlation and a significant positive correlation were seen for prevalence of subclinical mastitis versus total protein content or added water in bulk-tank milk. During multivariable analysis, younger age of newborns when taken away from the dam and consequently delayed start of milking of ewes, omission of anti-mastitis vaccination of ewes and lack of employed staff on the farms emerged to be significantly associated (positively) with increased incidence risk of subclinical mastitis.