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A cross sectional study was carried in Aloet Parish, Soroti district-Uganda to assess and quantify the prevalence of mastitis of lactating cows at cow level in the villages and udder quarter level for cows brought for sale at the Soroti livestock market. The objective was to acquire an empirical basis for stakeholders’ awareness in the small holder pastoral zones. Both clinical and subclinical mastitis were quantified at the village level and only SCM was considered at the market level. In the villages and the market SCM was tested using California Mastitis Test (CMT). In the villages of Aloet, 4 (12.5%) of the crosses and 60 (22.4%) Small East African zebu had mastitis. Overall, SCM and CM were at 50 (16.7%) and 14 (4.7%) occurrence and SCM was responsible for 78% of all the mastitis. Predisposing factors to mastitis among the pastoralists in communal grazing systems in Aloet were possibly habits such as stripping of teats using rough abrasion of fingers during milking coupled with none usage of milking salves. In the market, the right fore (RF) had a 34.2% (27/79) SCM and 1.25% (1/80) blind quarters. Right hind (RH) had a 30.8% (24/78) SCM and 2.5% (2/80) blind quarters. The left fore (LF) had a 36.6% (27/78) SCM and 2.5% (2/80) blind quarters. The left hind (LH) had a 31.4% (22/70) SCM and 12.5% blind quarters. The quarter prevalence rates were higher for the fore quarters than for the hind quarters. For all the quarters SCM prevalence was at 32.8% (100/305) and 4.9% (15/320) were blind. Bovine mastitis is an escalating hindrance to the upcoming dairy industry in agro-pastoral areas and requires urgent measures, SCM is possibly confounded by poor performance of local breeds and poor feeding management.