This study examined the socio-demographic, lifestyle, gynecological, and obstetric factors associated with serum or plasma concentrations of homocysteine, folic acid, and vitamins B12 and B6 among low-income women in São Paulo, Brazil. Serum concentrations of folic acid and vitamin B12 were measured by fluoroimmunoassay, while plasma vitamin B6 and homocysteine levels were measured by reversed-phase high performance liquid chromatography. Independent variables were initially selected by Pearson correlation or Kruskal-Wallis test (p < 0.20). Based on cut-off values, altered concentrations of homocysteine, folic acid, and vitamins B12 and B6 were found in 20%, 6%, 11%, and 67% of participants, respectively. Age was positively correlated with vitamin B6 and homocysteine plasma concentrations (p < 0.001). Body mass index was positively correlated with vitamin B6 plasma concentration (p < 0.001). Multiple linear regression models accounted for 10.2%, 5.8%, 14.4%, and 9.4% of folic acid, vitamins B12 and B6, and homocysteine plasma or serum concentrations, respectively. In this study, socio-demographic, lifestyle, gynecological, and obstetric variables showed important predictive value for serum or plasma levels of the biochemical indicators assessed.