The effects of interventions such as sanitation or hand hygiene on hand contamination are difficult to evaluate. We explored the ability of a simple microbiological test to: (1) detect recontamination after handwashing; (2) reflect risk factors for microbial contamination and (3) be applicable to large populations. The study was done in rural Andhra Pradesh, India, and Maputo, Mozambique. Participants placed all 10 fingertips on a chromogenic agar that stains Enterococcus spp. and E. coli spp. Outcomes were the number of colonies and the number of fingertips with colonies. In the recontamination study, participants were randomised to handwashing with soap and no handwashing, and tested at 30 min intervals afterwards. In two cross sectional studies, risk factors for hand contamination were explored. Recontamination of hands after washing with soap was fast, with baseline levels reached after 1 h. Child care was associated with higher Enterococcus spp. counts, whereas agricultural activities increased E. coli spp. counts. Food preparation was associated with higher counts for both organisms. In Maputo, counts were not strongly associated with water access, latrine type, education or diarrhoea. The method seems unsuitable for the evaluation of handwashing promotion. It may reflect immediately preceding risk practices but not household-level risk factors.