In 2010, a novel tick-borne pathogen called Candidatus Neoehrlichia mikurensis was first discovered in Europe. This bacterium can cause neochirlichiosis in humans and has mainly been restricted to immune compromised patients. In this report, blood samples from healthy patients taken during three-months follow-up visits to primary health care centers in South Central Sweden and Åland Islands, Finland were tested for the presence of Candidatus Neoehrlichia mikurensis. The blood was tested using a Real-time PCR assay targeting the bacteria groEL gene and screening showed that overall 2.25 % (3/133) of patients were infected. No significant differences in prevalence between geographic regions were observed. Phylogenetic analysis based on the groEL and 16S rRNA genes showed that bacterial sequences determined during this study formed a cluster together with other European Candidatus Neoehrlichia mikurensis sequences, and were distinct from those reported from Asia and North America. However, based on the conserved groEL and 16S rRNA genes, no distinct genotyping related to geographic sampling locations within Sweden and Åland Islands, Finland was observed. Due to the potential threats of infections with this bacterium in healthy patients, further studies of risk areas, tick vectors, zoonotic reservoir, and pathogenic mechanism are needed for this recently described bacterium.