The effects of congenital Zika syndrome (CZS) on the tooth development of infected children are not well known. The aim of this study was to analyze the association of CZS with dental alterations in children with microcephaly seen at a referral hospital in Rio Grande do Norte, Brazil. The chronology and sequence of tooth eruption and the presence of dental alterations were evaluated by a single calibrated examiner (kappa > 0.80) in 62 children aged 7 to 35 months with microcephaly associated with CZS and other congenital infections. Medical data of the mother and child were collected from the records and the parents responded to a socioeconomic questionnaire. Descriptive analysis and Fisher's exact test were used (5% significance level). The mean age of the children was 26.4 months (SD = 7.52). The mean weight and head circumference at birth were 2,593 g (SD = 0.60) and 29.6 cm (SD = 2.48), respectively. Microcephaly was associated with congenital Zika virus infection in 79% of cases and with other congenital infections in 21%. No significant association was found between CZS and alterations in the chronology (p = 1.00) or sequence of tooth eruption (p = 0.16) or changes in enamel development (p = 1.00). In conclusion, children with microcephaly exhibit a delay and alterations in the sequence of tooth eruption of primary teeth, as well as developmental defects of enamel, which are not associated with Zika virus infection.