Bangladesh is a country with a high burden of micronutrient malnutrition. Stunting affects 41 % of children aged under 5 years. Zn is one of the key micronutrients that is associated with stunting. The present study, as part of the national micronutrient survey 2011–2012, revealed for the first time the nationally representative prevalence of Zn deficiency and determined the associations of the condition. A cross-sectional ‘nationwide’ survey was conducted in pre-school-age children (6–59 months; PSAC) and non-pregnant non-lactating women (15–49 years; NPNLW). Multistage random sampling was done in 150 clusters; fifty in each of the rural, urban and slum strata. Data were analysed on 662 PSAC and 1073 NPNLW. Serum Zn was assayed by atomic absorption spectrophotometry. Zn deficiency was defined as serum Zn of <9·9 and <10·1 µmol/l in PSAC and NPNLW, respectively. The national prevalence of Zn deficiency was 44·6 and 57·3 % in PSAC and NPNLW, respectively. In PSAC, it was 29·5, 48·6 and 51·7 %, respectively, in urban, rural and slum strata. Household expenses (β = 0·13; P = 0·007), Hb (β = 0·10; P = 0·005), intake of animal-source Zn (β = 0·096; P = 0·02) and asset score (β = 0·11; P = 0·03) were positively associated with serum Zn in NPNLW. Residence in an urban area (β = 0·33; P = 0·03) and intake of plant-origin Zn (β = −0·13; P = 0·038) determined higher and lower status of Zn in PSAC, respectively. Zn deficiency was highly prevalent in Bangladesh, and it was principally related to inadequate quality of diet. To improve Zn nutrition, Bangladesh needs to strengthen research and programmes related to Zn biofortification, fortification and phytate-reducing technologies in the food system in the short and medium term. In addition, promotion of animal-source Zn for all is important in the long run.