Background: Donkeys in East Africa are recognized as working with poorly designed harnesses and carts. The donkey cart used in regions of Africa, specifically Meru County, Kenya, appears to place the cart’s weight solely on the donkey’s mid-cervical region where the trachea is superficially located. Objectives: To compare the presence and severity of endoscopic abnormalities in the upper airway and trachea of Meru County working cart donkeys compared to pack donkeys. To determine associations between endoscopic and external physical exam findings. Study design: Cross-sectional Methods: At voluntary health clinics, physical examination and endoscopy of the upper airway and trachea were evaluated and recorded at rest on 66 donkeys (38 cart donkeys and 28 pack donkeys). The presence and grade of tracheal collapse, tracheal ring abnormalities, tracheal mucous and pharyngitis were subsequently determined on the endoscopy recordings by blinded evaluators. Mann–Whitney and Chi-square/Fisher’s exact tests were used to investigate associations between work type and physical exam and endoscopy findings. Results: Significant associations were identified between work type and tracheal collapse severity, ring abnormalities, pharyngitis, skin lesions, and skin hypertrophy with these findings more common in cart than pack donkeys (all P<0.03). Moderate tracheal collapse (grade 3) was present in 40% (95% CI: 24-57%) of cart and 0% (0-12%) of pack donkeys. Exam findings were significantly and positively associated with endoscopy findings (all P<0.002). Main limitations: Standing endoscopy was performed at rest, not dynamic endoscopy during the pulling of carts. Conclusion: Moderate tracheal collapse was seen in cart donkeys when compared to pack donkeys. Physical exam findings at rest were associated with tracheal collapse and tracheal ring abnormalities. This work may help identify by physical examination donkeys that are at greatest need of improved harnesses.