Although the global burden of ear, nose and throat (ENT) diseases is high, data relating to ENT disease epidemiology and diagnostic error in resource-limited settings remain scarce. We conducted a retrospective cross-sectional review of ENT patients' clinical records at a resource-limited tertiary hospital. We determined the diagnostic accuracy and appropriateness of patient referrals for ENT specialist care using descriptive statistics. Cohens kappa coefficient (κ) was calculated to determine the diagnostic agreement between non-ENT clinicians and the ENT specialist, and logistic regression applied to establish the likelihood of patient misdiagnosis by non-ENT clinicians. Of the 1543 patients studied [age 0-87 years, mean age 25(21) years (mean(SD)], non-ENT clinicians misdiagnosed 67.4% and inappropriately referred 50.4%. Compared to those aged 0-5 years, patients aged 51-87 years were 1.77 (95%CI: 1.03-3.04) fold more likely to have a referral misdiagnosis for specialist care. Patients with ear (aOR: 1.63; 95% CI: 1.14-2.33) and those with sinonasal diseases (aOR: 1.80; 95% CI: 1.14-2.45) had greater likelihood of referral misdiagnosis than those with head and neck diseases. Agreement in diagnosis between the ENT specialist and non-ENT clinicians was poor (κ = 0.0001). More effective, accelerated training of clinicians may improve diagnostic accuracy in low-resource settings.