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Background/Objectives: The impact of daily variations in habitual maternal intake on human milk (HM) composition has been poorly studied. We aimed to investigate the associations between day-to-day fluctuation in the micronutrient concentration in HM and daily maternal diet. Methods: To this end, an observational longitudinal study was carried out. A total of 143 lactating women each compiled a five-day weighed dietary record and concomitantly expressed milk for four successive days. Maternal daily intakes of micronutrients and food groups were analyzed. Free thiamine, free riboflavin, nicotinamide, pantothenic acid, pyridoxal, folic acid, cobalamin, ascorbic and dehydroascorbic acids, retinol, alpha- and gamma-tocopherol, cholecalciferol, and calcidiol in HM were determined for each of the four investigated days. A longitudinal data analysis with generalized estimating equation models was performed. Results: For each daily serving of meat, fish, and eggs, total vitamin D3 levels increased by 243.2 pg/mL (p = 0.027) and selenium levels increased by 0.16 ppb (p = 0.031) in HM. For every 1 mg/day of riboflavin supplementation, free riboflavin levels in HM increased by 28.6 mcg/L (p = 0.019). Pyridoxal levels in HM increased by 6.3 mcg/L per 1 mg/day of vitamin B6 supplementation (p = 0.001), and by 2 mcg/L per daily fruit ration (p = 0.016). Conclusions: In conclusion, we were able to quantify the impact of the usual day-to-day variations in the diet and in the intake of commonly used supplements on the fluctuation of vitamin D, free riboflavin, pyridoxal, and selenium concentration in the milk of lactating women. [ABSTRACT FROM AUTHOR]