Micronutrient deficiencies compromise immune systems, hinder child growth and development, and affect human potential worldwide. Yet, to our knowledge, the only existing estimate of the global prevalence of micronutrient deficiencies is from over 30 years ago and is based only on the prevalence of anaemia. We aimed to estimate the global and regional prevalence of deficiency in at least one of three micronutrients among preschool-aged children (aged 6–59 months) and non-pregnant women of reproductive age (aged 15–49 years).