Background: Congenital infection is a primary cause of malformations during infancy including hydrocephaly and microcephaly. In addition, cytomegalovirus and toxoplasma are the two prevalent causes of congenital infections. The present research aimed to investigate the prevalence of cytomegalovirus and toxoplasma infections among neonates afflicted with microcephaly and hydrocephaly in a pediatric hospital in ۲۰۱۸.Materials and Methods: The present descriptive, cross-sectional research was conducted on all neonates diagnosed with microcephaly and hydrocephaly hospitalized in the pediatric hospital of Bandar Abbas in ۲۰۱۸. Blood samples were taken from the neonates to be analyzed for cytomegalovirus and toxoplasma serology, followed by statistically analyzing the information describing ۱۱ subjects including ۵ hydrocephaly and ۶ microcephaly cases.Results: The mean gestational age was estimated at ۳۵.۸ ± ۴.۰۸ and ۳۷.۱۶ ± ۱.۳۲ weeks in hydrocephaly and microcephaly groups, respectively (P = ۰.۵۰۷). In both groups, the female population was larger than the males. In addition, blood relations among parents were stronger in the microcephaly group (۴۰%) compared to the microcephaly group (۸۳.۳%). Moreover, the anomaly was found to be more in the microcephaly group. This rate was ۶۰% and ۱۶.۷% in the hydrocephaly and microcephaly groups, respectively. The serology of cytomegalovirus and toxoplasma in neither groups showed to be positive. One hundred percent of patients with an anomaly were term although ۵۰% of those without any anomaly belonged to the term group. It appears that the presence of an anomaly was positively correlated with term birth. One hundred percent of patients with an anomaly were found to have parents who were close relatives. However, ۵۰% of patients with no anomaly showed to have parents closely related in the family. Finally, heart problems were found to prevail in the group diagnosed with an anomaly.Conclusion: In the present research, the prevalence of cytomegalovirus and toxoplasma infections was reported to be zero in neonates who were afflicted with microcephaly and hydrocephaly.