Kazakhstan ranks ninth in the world in terms of country size. With its varied landscapes and hot and dry climate, it is a perfect home for many naturally occurring dangerous infectious diseases. Many of them are not well studied and due to the lack of contemporary diagnostic no or only poor differential diagnostics can be performed. Currently in Kazakhstan, most infectious diseases are diagnosed by physicians on an analysis of the clinical picture. Only in officially endemic areas for certain pathogens, physicians might be aware of the possibility of an infection with a pathogen, and only in these areas cases are publicly recorded. This system implies that there is a lack of reliable clinical laboratory diagnostics, trained laboratory staff and well-equipped laboratories all over Kazakhstan. In many cases, the aetiological agent cannot be determined, and patients with only having a fever, are diagnosed with fever of unknown origin. If patients’ symptoms also include headache, their diagnosis is suspected meningitis. In addition, the prevalence of many zoonoses is not well investigated in humans, hosts (like rodents) and vectors (like ticks). To address this issue, we investigated several viral and bacterial zoonotic pathogens in humans, rodents and ticks in areas of Kazakhstan that are not yet officially endemic for specific pathogens. The studies included viral pathogens belonging to the family of Flaviviridae like Omsk haemorrhagic fever virus (OHFV), Tick-borne encephalitis virus (TBEV) and West Nile virus (WNV). Also, Orthohantavirus and the bacterial genus of Rickettsia were investigated. The investigations were performed in human samples for OHFV, TBEV and WNV, in biopsies from small mammals for OHFV, Orthohantavirus, Rickettsia spp. and ticks for OHFV in several regions of Kazakhstan.