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[Background] Bisphenols, and especially bisphenol A, are widely used as components of epoxy resins and polycarbonate. Widespread detection and potential health risks have led to bisphenol A being replaced by other alternatives, including structurally similar bisphenol analogs. Several bisphenol analogs are suspected to have similar adverse health consequences. This study examined the temporal trends in bisphenol exposure among a group of Japanese women from 1993 to 2016, and assessed the associated health risks. [Methods] We used archived single spot urine samples of healthy Japanese women living in the Kyoto area (n = 133) collected in 1993, 2000, 2003, 2009, 2011, and 2016. We measured the concentrations of 10 bisphenols in these samples. [Results] A sharp increase in the detection rates of bisphenol F was observed after 2000. There was a distinct downward trend in urinary bisphenol A concentrations and an upward trend in bisphenol E concentrations after 2009. While the hazard index for all measured bisphenols was below 1 in all subjects, bisphenol F was determined as the most important risk driver after 2000, rather than bisphenol A. [Discussion] Trends of decreasing bisphenol A and increasing bisphenol E exposure especially after 2011, along with no significant change in the sum of all bisphenol analogs in urine, provide clear evidence that bisphenol A has been replaced by other bisphenols in the study population. We found no significant change in the total exposure to bisphenols during the study period. Bisphenol F might become the most important bisphenol in terms of risk, while cumulative risks due to all bisphenol exposure were deemed insignificant. Considering the accumulating evidence indicating adverse effects at lower exposure levels, further studies are warranted to assess exposure and risk from bisphenol A analogs.