Summary Background Loss‐of‐function mutations in the skin barrier gene filaggrin (FLG) increase the risk of atopic dermatitis (AD), but their role in skin barrier function, dry skin and eczema in infancy is unclear. Objectives To determine the role of FLG mutations in impaired skin barrier function, dry skin, eczema and AD at 3 months of age and throughout infancy. Methods FLG mutations were analysed in 1836 infants in the Scandinavian population‐based PreventADALL study. Transepidermal water loss (TEWL), dry skin, eczema and AD were assessed at 3, 6 and 12 months of age. Results FLG mutations were observed in 166 (9%) infants. At 3 months, carrying FLG mutations was not associated with impaired skin barrier function (TEWL > 11·3 g m−2 h−1) or dry skin, but was associated with eczema odds ratio (OR) 2·89, 95% confidence interval (CI) 1·95–4·28; P < 0·001. At 6 months, mutation carriers had significantly higher TEWL than nonmutation carriers mean 9·68 (95% CI 8·69–10·68) vs. 8·24 (95% CI 7·97–8·15), P < 0·01, and at 3 and 6 months mutation carriers had an increased risk of dry skin on the trunk (OR 1·87, 95% CI 1·25–2·80; P = 0·002 and OR 2·44, 95% CI 1·51–3·95; P < 0·001) or extensor limb surfaces (OR 1·52, 95% CI 1·04–2·22; P = 0·028 and OR 1·74, 95% CI 1·17–2·57; P = 0·005). FLG mutations were associated with eczema and AD in infancy. Conclusions FLG mutations were not associated with impaired skin barrier function or dry skin in general at 3 months of age, but increased the risk for eczema, and for dry skin on the trunk and extensor limb surfaces at 3 and 6 months. What is already known about this topic? Filaggrin (FLG) mutations are associated with the development of atopic dermatitis (AD). Dry skin is one of the main characteristics of AD and is associated with increased transepidermal water loss (TEWL). Impaired skin barrier function measured as increased TEWL has been shown to precede the development of AD. What does this study add? At 3 months of age, FLG mutations did not increase the risk of impaired skin barrier function or dry skin in general, but did increase the risk of eczema. At 6 months of age, higher TEWL was observed in FLG mutation carriers. At 3 and 6 months of age, carrying an FLG mutation was associated with dry skin on the trunk and extensor limb surfaces, but not with dry skin in general. What is the translational message? Our study highlights the genetic component in skin barrier function, dry skin, eczema and AD in early infancy. Linked Comment: D.J. Margolis. et al. Br J Dermatol 2022; 186:396. Plain language summary available online