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We aimed to estimate and compare within‐day energy balance (WDEB) in athletes with eumenorrhea and menstrual dysfunction (MD) with similar 24‐hour energy availability/energy balance (EA/EB). Furthermore, to investigate whether within‐day energy deficiency is associated with resting metabolic rate (RMR), body composition, S‐cortisol, estradiol, T₃, and fasting blood glucose. We reanalyzed 7‐day dietary intake and energy expenditure data in 25 elite endurance athletes with eumenorrhea (n = 10) and MD (n = 15) from a group of 45 subjects where those with disordered eating behaviors (n = 11), MD not related to low EA (n = 5), and low dietary record validity (n = 4) had been excluded. Besides gynecological examination and disordered eating evaluation, the protocol included RMR measurement; assessment of body composition by dual‐energy X‐ray absorptiometry, blood plasma analysis, and calculation …