There were 211,000 Indonesian Hajj pilgrims going to Mecca through 11 main airports in 2015 who were at risk of contracting the Middle East respiratory syndrome coronavirus (MERS-CoV). We aimed to find out whether there was any occurrence of MERS-CoV by performing screening on 28,197 returning pilgrims. Those with a body temperature of > 38 °C and respiratory symptoms were sent to the airport clinic to have an oropharyngeal swab and a bacterial culture. Fifteen pilgrims had fever (> 38 °C) accompanied by respiratory symptoms; of these, 12 patients were diagnosed with upper and lower respiratory tract infections and three patients with pneumonia. However, none of them were found to be infected with MERS-CoV. The bacterial cultures showed evidence of normal flora growth.