Background: Zika virus infection during pregnancy is linked to birth defects, most notably, microcephaly, which in its turn, is associated with neurodevelopmental delays. Objective: The goal of the study is to propose a method for severity classification of congenital microcephaly based on neuroradiological findings of MRI scans, and to investigate the association of severity with neuropsychomotor developmental scores. We also propose a semiautomated method for MRI-based severity classification of microcephaly. Methods: Cross-sectional investigation of 42 infants born with congenital Zika infection. Bayley-III developmental evaluations and MRI scans were carried out at ages 13-39 months (mean: 24.8, SD: 5.8). The severity score was generated based on neuroradiologist evaluations of brain malformations. Next, we established a distribution of Zika virusmicrocephaly severity score into mild, moderate, and severe and investigated the association of severity with neuropsychomotor developmental scores. Finally, we propose a simplified semi-automated procedure for estimating the severity score, based only on volumetric measures. Results: Results showed a correlation of r = 0.89 (p < 0.001) between the Zika virus-microcephaly severity score and the semi-automated method. The trimester of infection did not correlate with the semi-automated method. Neuropsychomotor development correlated with the severity classification based on radiological readings and with the semi-automated method; the more severe the imaging scores, the lower neuropsychomotor developmental scores. Conclusion: The severity classification methods may be used to evaluate severity of microcephaly and possible association with developmental consequences. The semi-automated methods thus may be an alternative for prediction of severity of microcephaly using only one MRI sequence.