To estimate direct medical costs (DMC) associated with treatment of Respiratory Distress Syndrome (RDS) in newborns (NB) in two specialized public hospitals in Mexico. The perspective used was health care payer. We estimated DMC associated with RDS management. The pattern of resource use was established by reviewing clinical records. Microcosting and bootstrap techniques were used to obtain the DMC. Estimated costs were reported in 2011 US dollars. Average DMC per RDS event was 14 226 USD. The most significant items that account for this cost were hospitalization (38%), laboratory and diagnostic exams (18%), incubator time (10%), surfactant therapy (7%), and mechanical ventilation (7%). Average DMC in NB with RDS fluctuated in relation to gestational age weight at birth and clinical complications presented by patients during their hospitalization.