Residents of urban slums are at greater risk for disease than their non-slum dwelling urban counterparts. We sought to contrast the prevalences of selected non-communicable diseases (NCDs) between Brazilian adults living in a slum and the general population of the same city, by comparing the age and sex-standardized prevalences of selected NCDs from a 2010 survey in Pau da Lima, Salvador Brazil, with a 2010 national population-based telephone survey. NCD prevalences in both populations were similar for hypertension (23.6% (95% CI 20.9–26.4) and 22.9% (21.2–24.6), respectively) and for dyslipidemia (22.7% (19.8–25.5) and 21.5% (19.7–23.4)). Slum residents had higher prevalences of diabetes mellitus (10.1% (7.9–12.3)) and of overweight/obesity (46.5% (43.1–49.9)), compared to 5.2% (4.2–6.1) and 40.6% (38.5–42.8) of the general population in Salvador. Fourteen percent (14.5% (12.1–17.0)) of slum residents smoked cigarettes compared to 8.3% (7.1–9.5) of the general population in Salvador. The national telephone survey underestimated the prevalence of diabetes mellitus, overweight/obesity, and smoking in the slum population, likely in part due to differential sampling inside and outside of slums. Further research and targeted policies are needed to mitigate these inequalities, which could have significant economic and social impacts on slum residents and their communities.