The objective of this study is to evaluate whether daily clinic visits for conjunctivitis are associated with the ambient environment in urban and rural areas of Taiwan. The incidences of acute and chronic conjunctivitis (International Classification of Disease 9 Clinical Modification 372.0 and 372.1) in two urban cities and two rural counties and their relative risks (RRs) are associated with air pollutants (nitrogen oxides (NOx), sulfur dioxide, ozone, and particulate matter <10 μm in aerodynamic diameter) and/or weather statuses were assessed from the insurance reimbursement claims of a representative 1 million people from 2000 to 2007. The patients resided in rural counties were approximately eight time more likely to have acute complains and >1.3 time more likely to have chronic complaints than the patients lived in the capital, Taipei. Per 10 °C increment of the daily average temperature increased the risk of acute conjunctivitis and chronic conjunctivitis with RRs of 1.06 (95% confidence interval (CI): 1.03-1.09) and 1.05 (95% CI: 1.04-1.07), respectively. A 10-p.p.b. increase in NOx concentration also increased the risk of acute conjunctivitis (RR=1.03, 95% CI: 1.02-1.04) and chronic conjunctivitis (RR=1.06, 95% CI: 1.05-1.06). Residents in rural counties, females, the elderly, and children have higher risk of conjunctivitis. Ambient temperature and NOx concentration can cause greater significant risks on the diseases.