Clinical mastitis (CM) is an important production disease in dairy cows, but much of the knowledge required to effectively control CM is lacking, specifically in low-income countries where most farms are small and have specific dairy management, such as regular udder cleaning and practicing hand milking. Therefore, we conducted a 6-month-long cohort study to (a) estimate the incidence rate of clinical mastitis (IRCM) at the cow and quarter level, (b) identify risk factors for the occurrence of CM, (c) describe the etiology of CM, and (d) quantify antimicrobial susceptibility (AMS) against commonly used antimicrobial agents in S. aureus and non-aureus Staphylococcus spp. (NAS) in dairy farms in the Chattogram region of Bangladesh. On 24 farms, all cows were monitored for CM during a 6-month period. Cases of CM were identified by trained farmers and milk samples were collected aseptically before administering any antimicrobial therapy. In total, 1383 lactating cows were enrolled, which totaled 446 cow-years at risk. During the study period, 196 new cases of CM occurred, resulting in an estimated crude IRCM of 43.9 cases per 100 cow-years, though this varied substantially between farms. Among the tested CM quarter samples, Streptococci (22.9%) followed by non-aureus staphylococci (20.3%) were the most frequently isolated pathogens and resistance of S. aureus and NAS against penicillin (2 out of 3 and 27 out of 39 isolates, respectively) and oxacillin (2 out of 3 and 38 out of 39 isolates, respectively) was common. The IRCM was associated with a high milk yield, 28 to 90 days in milk, and a higher body condition score. Our results show that there is substantial room for udder health improvement on most farms.