Longitudinal studies were carried out to determine trends in CD4 cell counts over a four year period in healthy HIV-negative adults in a rural (134 individuals) and an urban (80 individuals) site in Malawi, using TruCountTM and FACScountTM platforms. At baseline, median counts and 95% ranges were 890 (359-1954) cells per microlitre (μl) and 725 (114-1074) cells/μl respectively. 1.5% and 6% respectively had baseline counts below 350 cells/μl and 1.5% and 2.5% below 250 cells per μl. Transient dips to below 250 cells/μl were observed in seven individuals, with two individuals having persistently low CD4 counts over more than one year. Women and individuals from the urban site were significantly more likely to have "low CD4 count" (< 500 cells/μl) even when adjusted for other factors. In common with neighbouring countries, HIV-negative populations in Malawi have CD4 counts considerably lower than European reference ranges, and healthy individuals may have persistently or transiently low counts. Within Malawi, ranges differ according to the selected population.