Among the many challenges to health, infectious diseases stand out for their ability to have a profound impact on humans and animals. The recent years have witnessed an increasing number of novel infectious diseases. The numerous examples of infections which originated from animals suggest that the zoonotic pool is an important and potentially rich source of emerging diseases. Since emergence and re-emergence of pathogens, and particularly zoonotic agents, occur at unpredictable rates in animal and human populations, infectious diseases will constitute a significant challenge for the public health and animal health communities in the twenty-first century. The African continent suffers from one of the highest burdens of infectious diseases of humans and animals in the world but has the least capacity for their detection, identification and monitoring. Lessons learnt from recent zoonotic epidemics in Africa and elsewhere clearly indicate the need for coordinated research, interdisciplinary centres, response systems and infrastructures, integrated surveillance systems and workforce development strategies. More and stronger partnerships across national and international sectors (human health, animal health, environment) and disciplines (natural and social sciences) involving public, academic and private organisations and institutions will be required to meet the present and future challenges of infectious diseases. In order to strengthen the efficiency of early warning systems, monitoring trends and disease prediction and timely outbreak interventions for the benefit of the national and international community, it is essential that each nation improves its own capacity in disease recognition and laboratory competence. The SACIDS, a One Health African initiative linking southern African academic and research institutions in smart partnership with centres of science excellence in industrialised countries as well as international research centres, strives to strengthen Africa's capacity to detect, identify and monitor infectious diseases of humans and animals, to better manage health and socio-economic risks posed by them, and to improve research capacity in investigating the biologic, socio-economic, ecologic and anthropogenic factors responsible for emergence and re-emergence of infectious diseases.