For newborns and neonates, ultrasound (US) is the most common imaging modality used for examinations due to its accessibility and ease of use. However, precise volume measurements remain limited in 2D, while MRI in newborns is typically avoided because of immobilization issues which may require sedation. The objective of this study is to assess and validate the lateral ventricular and total brain volumes obtained with an automatic segmentation method using cerebral trans-fontanelle 3D US. Infants aged between 2 and 8.5 months old were recruited, with both MRI and 3D US acquired on the same day was used to validate ventricular and brain volume measurements in comparison to MRI. Lateral ventricles were segmented on both the US (manually and with a proposed automatic fusion-based approach) and MRI, while brain volumes were estimated with an automatic segmentation method. Volumetric 3D US measurements were then evaluated with respect to age distribution. For the comparison between MRI and 3D US, strong inter-class correlations (ICC) were found for the ventricle volumes (manual: 5.9% ± 2.5% difference (ICC = 0.99); automatic: 6.0% ± 2.6% difference (ICC = 0.98)), as well as the total brain size, with a 3.0% ± 1.3% difference (ICC = 0.98). There was no statistically significant difference based on t-test and f-test for the lateral ventricles volume (t-test: p = 0.542) and (f-test: p = 0.738) and for the total brain volume (t-test: p = 0.412) and (f-test: p = 0.685) between MRI and 3D US. This study demonstrates that 3D US can be used to automatically assess lateral ventricular and total brain volumes with no significant difference to the MRI acquisitions. The highest correlations were obtained for infants under 8 months when the fontanelle is open.