Horses are used for a wide variety of purposes from being used for recreational purposes to competing at an international level. With these different uses, horses have to adapt to numerous challenges and changes in their environment, which can be a challenge itself in continuously safeguarding their welfare. The objective of this study was to assess the prevalence of health disorders with clinical examination and identify possible risk factors of health disorders affecting horse welfare in professional husbandry systems in the Netherlands. With the use of fixed protocols for recording health aspects in horses, 150 horse farms voluntarily participating in the study were assessed by trained assessors. On each farm, 20 horses were clinically examined, in total almost 3,000 animals. This study recorded on the basis of the clinical examinations: the respiratory system (i.e., abnormal breathing [1%], coughing [1%], nasal discharge [1.9%]), body condition (i.e., 18.8% fat body condition and 6.4% poor body condition), locomotion (14.5% exhibited irregularity of locomotion and 4.8% were lame), back palpation (a light response [22.6%] and moderate to severe response [8.4%]), mouth (i.e., irregularities on mouth corners [3.4%] and bars [3.4%]), and ocular discharge (12%). Risk factor analysis, stepwise using mixed model regression, demonstrated several risk factors for health aspects. Horses used for instruction (riding lessons) were almost two times more at risk to develop moderate to severe back pain compared to horses used for recreation (odds ratios [OR] = 0.54) or for competition (OR = 0.61). Horses used for instruction (riding school lessons), breeding, or recreation all had a higher risk for irregular locomotion or lameness compared to competition horses (OR = 0.42, OR = 0.55, OR = 2.14, respectively). Horses used for recreation were more prone to have a higher BCS compared to horses used for breeding (OR = 3.07) and instruction (OR = 2.06). The prevalence of health problems and the identified risk factors are valid ...