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Background: Scrub typhus is an endemic disease in Asia. It has been a rural disease, but indigenous urban cases have been observed in Seoul, South Korea. Urban scrub typhus may have a significant impact because of the large population. Methods: Indigenous urban scrub typhus was epidemiologically identified in Seoul, the largest metropolitan city in South Korea, using national notifiable disease data from 2010 to 2013. For detailed analysis of clinical features, patients from one hospital that reported the majority of cases were selected and compared to a historic control group. Chigger mites were prospectively collected in the city using a direct chigger mite-collecting trap, and identified using both phenotypic and 18S rDNA sequencing analyses. Their infection with Orientia tsutsugamushi was confirmed by sequencing the 56-kDa antigen gene. Results: Eighty-eight cases of urban scrub typhus were determined in Seoul. The possible sites of infection were mountainous areas (56.8%), city parks (20.5%), the vicinity of one's own residence (17.0%), and riversides (5.7%). Eighty-seven chigger mites were collected in Gwanak mountain, one of the suspected infection sites in southern Seoul, and seventy-six (87.4%) of them were identified as Helenicula miyagawai and eight (9.2%) as Leptotrombidium scutellare. Pooled DNA extracted from H. miyagawai mites yielded O. tsutsugamushi Boryong strain. Twenty-six patients from one hospital showed low APACHE II score (3.4 ± 2.7), low complication rate (3.8%), and no hypokalemia. Conclusions: We identified the presence of indigenous urban scrub typhus in Seoul, and a subgroup of them had mild clinical features. The chigger mite H. miyagawai infected with O. tsutsugamushi within the city was found. In endemic area, urban scrub typhus needs to be considered as one of the differential febrile diseases and a target for prevention. Author Summary: Scrub typhus is one of the high burdened infectious diseases in endemic rural areas. Our study showed that the disease could be endemic in urban areas. Indigenous urban scrub typhus may also have significant impact in terms of a disease burden and differential diagnosis. A low rate of characteristic eschar and skin rash may make the clinical suspicion more troublesome. Scrub typhus is the 3rd most frequent notifiable infectious disease in South Korea. Seoul is a densely populated capital city located in northwestern South Korea. We epidemiologically identified indigenous urban cases. A subgroup of them showed mild clinical characteristics. Direct mite collection from a suspected infection site, Mt. Gwanak in Seoul, showed that Helenicula miyagawai (87.4%) and Leptotrombidium scutellare (9.2%) were the dominant species. In addition, O. tsutsugamushi-specific gene, tsa56, was identified in a fraction of the collected H. miyagawai. The 18S rDNA sequencing of the chigger mites was complementarily helpful for the differentiation of species. Our data are from one region, but urban scrub typhus is likely a scenario in endemic areas. Urban areas should be included as possible locations for scrub typhus. [ABSTRACT FROM AUTHOR]