Urban segregation has brought significant challenges to cities worldwide and has important implications for health. This study aimed to assess income segregation in the 152 largest Brazilian cities included in the SALURBAL Project and identify specific socioeconomic characteristics related to residential segregation by income. Using the Brazilian demographic census database of the year 2010, we calculated the income dissimilarity index (IDI) at census tract level for each SALURBAL city; subsequently comparing it with Gini and other local socioeconomic variables. We evaluated our results' robustness using a bootstrap correction to the IDI to examine the consequences of using different cut-offs of income that were relevant in the context of strong urban and regional inequalities. We identified a 2 minimum wages cut-off as the most appropriate and found little evidence of upward bias in the calculation of the IDI regardless of the cut-off used. Among the 10 most segregated cities, 9 are in the Northeast region, the region with the highest income inequality and poverty in Brazil. Our results indicate that the Gini index and poverty are the main variables associated with residential segregation, measured by the IDI. Social and environmental characteristics were also associated with IDI, reinforcing the notion that access to education, water, sanitation, and better residential conditions are fundamental to improving social equity.