Objectives Few studies have reported on the association between changes in serum low‐density lipoprotein cholesterol (LDL‐C) and height increase. We investigated the association between LDL‐C change and height increase during puberty in a 3‐year follow‐up study in Fukuroi City, Japan. Methods The source population was all fifth grade 2,515 students enrolled in any public school in Fukuroi, Japan in 2008, 2009, and 2010. The follow‐up survey was conducted in eighth grade students in 2011, 2012, and 2013. In total, 2,225 adolescents were followed. To evaluate the relationships between height increases and changes in LDL‐C, a regression analysis was conducted after stratification by tertiles of weight change (LW: lowest group, MW: middle group, and HW: highest group). Results In each weight change tertile, serum LDL‐C significantly decreased from the lowest to highest tertiles of height change (LW: regression coefficient (B) = −0.12, MW: B = −0.07, HW: B = −0.08 in males; MW: B = −0.17, HW: B = −0.14 in females). The association between height increases and LDL‐C was significantly stronger than that between weight increases and LDL‐C (male: B = −0.609 and 95% CI −0.836 to −0.382 in height, B = 0.008 and 95% CI −0.193 to 0.209 in weight; female: B = −0.963 and 95% CI −1.301 to −0.624 in height, B = 0.366 and 95% CI 0.058–0.675 in weight). Conclusions Serum LDL‐C decreased with increasing height, independent of increases in weight. The association between LDL‐C and height is stronger than that between LDL‐C and weight. Am. J. Hum. Biol. 28:330–334, 2016. © 2015 Wiley Periodicals, Inc.