Congenital microcephaly can be the result of genetic, teratogenic, mechanical, infectious, and other factors affecting the fetal brain. Transient craniofacial asymmetries and cranial molding can mimic congenital microcephaly caused by brain abnormalities or neurotropic infectious pathogens, including Zika. We present two neonates who were born with head circumference at or below the 3rd percentile for gestational age, and had improving head measurements at discharge from the nursery and resolution of the microcephaly by the second month of life. The diagnostic workup of the first patient revealed congenital cranial bone asymmetry and molding, and the second patient's workup revealed cranial molding. Other etiologies for their microcephaly were excluded. These two cases highlight the importance of standardized serial head circumference measurements as part of the workup for neonatal microcephaly. Clinical exclusion of transient congenital craniofacial asymmetries and cranial molding could be a cost-effective first step in the diagnostic workup of microcephaly.