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Japan, which currently maintains the highest life expectancy in the world and has experienced an impressive gain in adult height over the past century, has suffered a dramatic twofold increase in low birth weight (LBW) births since the 1970s.We observed secular trends in birth characteristics using 64 115 249 live births included the vital statistics (1969–2014), as well as trends in average height among 3 145 521 adults born between 1969 and 1996, included in 79 surveys conducted among a national, subnational or community population in Japan.LBW rates exhibited a U-shaped pattern showing reductions until 1978–1979 (5.5%), after which it increased. Conversely, average adult height peaked for those born during the same period (men, 171.5 cm; women, 158.5 cm), followed by a reduction over the next 20 years. LBW rate and adult height showed a strong inverse correlation (men, r=−0.98; women, r=−0.88). A prediction model based on birth and economical characteristics estimated the national average of adult height would continue to decline, to 170.0cm (95% CI 169.6 to 170.3) for men and 157.9cm (95% CI 157.5 to 158.3) for women among those born in 2014.Adult height in Japan has started to decline for those born after 1980, a trend that may be attributed to increases in LBW births over time. Considering the known association between shorter adult height and adverse health outcomes, evidence of population-level decline in adult health due to long-term consequences of increasing LBW births in Japan is anticipated.