Most research on hypothalamic-pituitary-adrenal axis function under aversive conditions has focused on relatively increased acute episodic, or chronic secretions as an operationalization of “stress.” Severe or recurrent stress, perhaps in interaction with individual characteristics, results in chronically decreased HPA function among some persons suffering from posttraumatic stress disorder. Little evidence exists to assess the population distribution of chronic low cortisol in different free-ranging human populations, as a manifestation of past trauma or stress. This study reports findings of chronically depressed ambulatory salivary cortisol among rural-dwelling Batswana men (n=30) compared with men living in Gaborone (n=34), the capital of Botswana, based on repeated ambulatory sampling. Out of 914 saliva samples analyzed by radioimmunoassay, 268 (29.3%) samples (41 urban, 227 rural) were below the minimum detectable dose (<MDD of 0.034 ug/dL) of the assay. Low values were distributed across comparable times of day as were =MDD samples. There was significant clustering of low cortisol within individuals; percentage of intra-individual repeats that were <MDD ranged from zero to 94.1% for rural participants (median=59.8%; mean=54.8%; SD=27.8%), and from zero to 40% for urban (median=0%; mean=8%; SD=11.9%). There was no association between number of repeats and proportion <MDD (P[F=−0.47]=0.639; β₁=−0.0045±0.0019). Examination of laboratory quality control suggests that this pattern is not a result of measurement error, or poor sample preservation, but instead reflects a difference from residing in a remote rural versus a central urban community.