Abstract: 　Objective　To explore the clinical characteristics of neonatal Mycoplasma pneumoniae pneumonia (MPP) and Chlamydia trachomatis pneumonia (CTP). Method　The clinical data of neonatal MPP and CTP which diagnosis was confirmed from January 2013 to December 2016 were analyzed, and the newborns with other infectious pneumonia were selected as controls of MPP group and CTP group respectively according to the matching standard. Results　There were 44 cases in MPP group, 30 cases in CTP group, 88 cases in MPP control group and 60 cases in CTP control group. In 44 cases of MPP group, 17 cases had the history of contact with respiratory infection patients (38.6%), 44 cases had cough (100.0%), 16 cases had fever (36.4%), 16 cases had diarrhea (36.4%), 10 cases had respiratory failure (22.7%), 9 cases had type II respiratory failure (20.5%), 4 cases had segmental consolidation (9.1%) and 5 cases had interstitial change (11.4%). The incidence rates above were higher than those in its control group, and the differences were statistically significant (P<0.05). In the 30 cases of CTP group, 26 cases were vaginal delivery (86.7%), 11 cases had premature rupture of membranes (36.7%), 28 cases had cyanosis (93.3%), 13 cases had diarrhea (43.3%), and 11 cases had eye secretion (36.7%). The incidence rates above were higher than those in the control group, and there were statistical differences (P<0.05). The proportion of vaginal delivery in CTP group was higher than that in MPP group, and the proportion of patients with the history of contact with respiratory tract infection patients was lower than that in MPP group , and there were statistical differences (P<0.05). Fever, cough, anhelation and fine wet rales were more common in MPP group than those in CTP group, and cyanosis and eye secretion were more common in CTP group than those in MPP group, and there were statistical differences (P<0.05). Patients in MPP group and CTP group were treated with macrolide antibiotics, and all of them were improved and discharged without any death. Conclusion　Neonatal MPP is more susceptible to fever, cough, anhelation and fine wet rale in the lungs. The neonatal CTP is more likely to have cyanosis and eye secretions. Macrolide antibiotics can be used in both of them, and the prognosis is good.