Background: Herpes virus group can persist in the latent form in the body, Pneumocystis jerovecii, on the other hand, is a fungus which is ubiquitous in the respiratory tract of mammals, with 90% of adult human beings possessing antibodies to this organism. Concomitant presence of different microorganisms, may result in one microorganism altering the activity of another.Objectives: To determine the frequency of 5 latent Herpes viruses and Pneumocystis jirovecii and to ascertain the rate of concomitant presence of these microorganisms in saliva of healthy children.Patients and Methods: This cross-sectional study was performed on 150 immune-competent children 1 to 15 years old visited in the outpatient clinics at a university-affiliated children’s hospital from 22nd May to 21st August 2011. Samples of saliva obtained from the children were subjected to DNA extraction by polymerase chain reaction.Results: At least one microorganism was isolated from saliva of 148 children, (98.6%). In 13 cases only 1 microbe was detected, (8.6%), 2 pathogens were isolated from 24 children, (16%), 3 from 20 cases, (13.3%), 4 from 54 individuals (36%), and 5 from 37 subjects (54.4). HSV was the most frequent organism detected in 80.7%, and P. jirovecii the least frequent, (32.7%). Other viruses were HHV6, 66.7%, CMV 66.0%, HHV7 64.7%, and EBV 37.3% in order. No significant difference was found in the frequency of microorganisms in the two sexes or in different age groups, except for CMV which was significantly less frequent in age group of 6-10 years (P value=0.001).Regression analysis revealed an association between HHV6 and HHV7 (OR=1599.4; P value<0.001); a correlation was also found between EBV and CMV (OR=3.1; P value=0.012). In contrast, a negative correlation was found between P. jirovecii and three viruses of the Herpes virus group including EBV (OR=0.27; P value=0.006), HSV1 (OR=0.36; P value=0.028), and CMV (OR=0.48; P value=0.075).Conclusions: Shedding of latent Herpes viruses and concomitant presence of multiple inactive micro-organisms is common in saliva of immune-competent children.