BACKGROUND: Biometric fingerprint identity verification is currently introduced in visa application and entry screening at border control. The system implies physical contact between the skin and the surface of the fingerprint-capturing and reading devices. AIM: To assess the risk of infection transmission through fingerprinting. METHODS: The medical literature was reviewed for the potential of microorganisms to be carried on the skin of hands in the community, to be transferred from hands to inanimate surfaces, to survive on surfaces, and to be transferred in doses exceeding the infectious dose. The fingerprinting procedures as currently applied were reviewed. RESULTS: Factors that favor transfer of microorganisms are large skin-surface contact between flat fingers (2 x 20 cm(2)) and fingerprint-capturing device, nonporous contact surface, large overlap of contact surface and short turnaround time between successive applicants, high contact pressure, and difficulties to disinfect devices. Transmission risk exists for enteric viruses (rotavirus, norovirus, and hepatitis A virus), respiratory viruses (respiratory syncytial virus, rhinovirus, influenza virus, etc.), and enteropathogenic bacteria with low infectious doses (Shigella dysenteriae, Enterohemorrhagic Escherichia coli, etc.). Using Monte Carlo risk analysis on US data, transmission of human rotavirus is estimated at 191 [95% credible intervals (CI) 0-289] per million fingerprint-capturing procedures. Application of 70% isopropyl hand rub and 85% ethanol hand gel reduces the risk to 77 (95% CI 0-118) and 0.3 (95% CI 0-0.3) transmissions per million procedures, respectively. CONCLUSIONS: The fingerprinting procedure as currently used is associated with a risk of infection transmission. Simple hygienic measures can considerably reduce this transmission risk.