A male child, maintained in a controlled environment, was monitored each month for bacteria, yeasts, and filamentous fungi recovered from the mouth, nasal passages, feces, and nine body surface sites. Three natural microbial categories became apparent. (i) Incident microorganisms were recovered from within the isolator but did not establish permanent residence. Of the 53 incident types isolated, 20 were filamentous fungi and 4 were yeasts. Some genera, such as Fusobacterium, Lactobacillus, Neisseria, and Rothia, which were commonly found in the reference group, did not become permanent inhabitants. (ii) Transient microorganisms were repeatedly recovered but could not be demonstrated within the isolated environment at the end of the study. The loss of only a few of the 19 transient species could be associated with antimicrobial therapy. (iii) Permanent microorganisms consisted of Pencillium citrinum and 17 bacterial types, of which alpha-hemolytic streptococci, Staphylococcus edpidermidis subgroups II and V, Micrococcus groups 1 and 2, Clostridium bifermentans, and Propionibacterium acnes were recovered throughout the entire 9 years of the study. The number of CFUs recovered from each sample type was generally not unlike that from the reference group of healthy male adults. Also, the number of different aerobic species recovered from the feces was within the normal range of that of the reference group. In contrast, the number of different species recovered from all other samples was less than that commonly found in the reference group.