Pneumocystis pneumonia may be fatal in Premature, seriously ill infants at intensive care units. Our aim was to evaluate the routine treatment applied in Sohag pediatrics department for neonatal and infantile pneumonia (in NICU & PICU) on PCP and to compare between the stained slides and real time-PCR in diagnosing Pneumocystis jirovecii. Subjects and methods: Sucked sputum from 21 pneumonic neonates (n=9) & infants (n=12) was collected, each divided in 2 parts, part for Giemsa stain and microscopic examination and the rest for PCR. The same procedure was done after regression of the symptoms and before release from the units. Serum samples were also collected on admission and discharge for CRP readings which were also used as an indicative of the healing process. The results: out of the 21 pneumonic neonates & infants examined, 12 (57.1%) showed P. jirovecii in their sputum samples (6 from each group) with a significant difference between the two groups (p=0.2). 10 of them (83.3%) became negative for p. jirovecii after the routine regimen of treatment. There were also 2 cases infected with microspora, both in infants and both were cured after treatment. While real time PCR was negative in all cases pre and post treatment. CPR levels regressed after treatment in all cases except 2, one of them, showed post treatment P.jirovecii in the sputum. Conclusions: Routine treatment for infant pneumonia was successful in treating microspora and significantly successful for treating P.jirovecii (P=0.00). Real time PCR failed to diagnose P.jirovecii local strain.