In 2005 we evaluated a nationally representative sample of the Mozambican adult population (n = 2913; 25–64 years old) following the STEPwise approach to chronic disease risk factor surveillance to estimate urban–rural differences in overweight and obesity and waist circumferences. The prevalences of obesity and overweight were, respectively, 6.8% (95% CI: 5.1–8.6) and 11.8% (95% CI: 8.4–15.4) among women, and 2.3% (95% CI: 1.1–3.6) and 9.4% (95% CI: 5.7–13.1) among men. Overweight/obesity was more frequent in urban settings (age-, income- and education-adjusted prevalence ratios; women, 2.76, 95% CI: 1.82–4.18; men, 1.76, 95% CI: 0.80–3.85). The average waist circumference in Mozambique was 75.2 cm (95% CI: 74.3–76.0) in women, significantly higher in urban than rural areas (age-, income- and education-adjusted β = 3.6 cm, 95% CI: 1.6–5.5) and 76.1 cm (95% CI: 75.0–77.3) in men, with no urban–rural differences (adjusted β = 1.3 cm, 95% CI: −0.9 to 3.5). Our results show urban–rural differences, as expected in a country under epidemiological transition, with urban areas presenting a higher prevalence of overweight/obesity, but age- and education-specific estimates suggesting a trend towards smaller divergences. The development and implementation of strategies to manage the foreseeable obesity-related healthcare demands are needed.