Desert dust is considered to be potentially toxic and its toxicity may change during long-range transportation. In Asian countries, the health effects of desert dust in different locations are not well understood. We therefore evaluated the city-combined and city-specific effects of Asian dust events on all-cause and cause-specific mortality in five populous cities in South Korea (Seoul) and Japan (Nagasaki, Matsue, Osaka and Tokyo). We obtained daily mean concentrations of Asian dust using light detection and ranging (lidar) between 2005 and 2011. We then evaluated city-specific and pooled associations of Asian dust with daily mortality for elderly residents (≥65 years old) using time-series analyses. Each 10 μg/m3 increase in the concentration of same-day (lag 0) or previous-day (lag 1) Asian dust was significantly associated with an elevated pooled risk of all-cause mortality (relative risk (RR): 1.003 [95% CI: 1.001-1.005] at lag 0 and 1.001 [95% CI: 1.000-1.003] at lag 1) and cerebrovascular disease (RR: 1.006 [95% CI: 1.000-1.011] at lag 1). This association was especially apparent in Seoul and western Japan (Nagasaki and Matsue). Conversely, no significant associations were observed in Tokyo, which is situated further from the origin of Asian dust and experiences low mean concentrations of Asian dust. Adverse health effects on all-cause and cerebrovascular disease mortality were observed in South Korea and Japan. However, the effects of Asian dust differed across the cities and adverse effects were more apparent in cities closer to Asian dust sources.