Introduction Anemia is a very frequent event among pregnant women. There are evidences of differences in the incidence of dental caries between pregnant and non-pregnant women, but the relationship between salivary iron (Fe) and serum markers of anemia and caries development has not been investigated. Objective To evaluate the correlation between salivary (Fe) and serum iron (Fe, ferritin and hemoglobin) parameters in pregnant women with the development of dental caries. Methods A prospective cohort was conducted with 59 women. The outcome of interest was represented by new dental caries lesions during pregnancy, using the Nyvad criteria. Pregnant women were evaluated at three clinical times: up to the 16th week of gestational age (GA) (T1), in the last trimester of pregnancy (T2), and postpartum (T3), at the Mother and Child Unit of University Hospital of the Universidade Federal do Maranhão. A stimulated saliva sample was collected for biochemical analysis of salivary Fe, and a blood sample was collected early in the morning. The correlation between salivary and serum Fe was evaluated through the Pearson correlation test. Analysis of variance (ANOVA) and Kruskal-Wallis were used to compare the means of anemia parameters at different times. The Student's t and Mann-Whitney tests were used to compare the anemia parameters between the groups of pregnant women (with and without new caries lesions). Results Serum Fe concentrations were higher in the first trimester of pregnancy and lower after delivery (p = 0.036). It was also observed that the ferritin concentrations were higher in the first trimester and lower at the end of gestation (p = 0.011). There was no association between the expositions of salivary iron and anemia, and the development of dental caries. There was a positive correlation between serum Fe in T1 and salivary Fe in T2 (p < 0.05). Conclusion The serum markers of anemia were more prevalent in the last trimester of pregnancy.