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Lyme disease, recognized as one of the most important vector-borne diseases worldwide, has been increasing in incidence and spatial extend in United States. In the Northeast and Upper Midwest, Lyme disease is transmitted by Ixodes scapularis . Currently, many studies have been conducted to identify factors influencing Lyme disease risk in the Northeast, however, relatively few studies focused on the Upper Midwest. In this study, we explored and compared the climatic and landscape factors that shape the spatial patterns of human Lyme cases in these two regions, using the generalized linear mixed models. Our results showed that climatic variables generally had opposite correlations with Lyme disease risk, while landscape factors usually had similar effects in these two regions. High precipitation and low temperature were correlated with high Lyme disease risk in the Upper Midwest, while with low Lyme disease risk in the Northeast. In both regions, size and fragmentation related factors of residential area showed positive correlations with Lyme disease risk. Deciduous forests and evergreen forests had opposite effects on Lyme disease risk, but the effects were consistent between two regions. In general, this study provides new insight into understanding the differences of risk factors of human Lyme disease risk in these two regions., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.