The continuing state of conflict and the resulting devastation of infrastructure have made Afghanistan exceptionally vulnerable to disease epidemics. The paper reports initiatives by the United States Naval Medical Research Unit No. 3 to promote capacity building in a number of key medical laboratories and enable the Afghans to detect emerging and re-emerging diseases of public health importance. Equipment, supplies and laboratory staff training were critical for disease diagnosis and fulfilment of obligations of the International Health Regulations 2005. Accordingly, many diseases outbreaks were recently identified, including avian and pandemic influenza, febrile illness, watery diarrhoea, jaundice and leishmaniasis. Clinical samples and disease vectors were collected for analysis, and microbial isolates were obtained for further characterization. The expanded range and enhanced accuracy of laboratory procedures have facilitated selected local laboratories to monitor, detect, identify, assess, contain and respond to public health threats. Nevertheless, policies of sustainability and infectious diseases control need continuous support and emphasis.