Brain scans of 23 Brazilian infants with the birth defect microcephaly showed widespread and severe abnormalities suggesting that Zika may invade foetal nerve cells and disrupt brain development.
The findings, published in a letter to the New England Journal of Medicine, are based on a large trove of computed tomography, or CT images, done in infants whose mothers are believed to have had Zika infections during pregnancy.
The study included researchers from Brazil's Northeastern state of Pernambuco, such as Dr Ana van der Linden of the Instituto de Medicina Integral, who were among the first to sound the alarm about increasing cases of microcephaly in Brazil thought to be linked with Zika infections.
Microcephaly is a typically rare birth defect marked by unusually small head size, signalling a problem with brain development.
Brazil is investigating thousands of cases of microcephaly and has confirmed more than 940 cases to be related to Zika infections in the mothers.
Scientists in the study ran several tests on the mothers to try to rule out other possible causes of microcephaly, including toxoplasmosis, cytomegalovirus, parovirus, HIV and rubella.
All were all negative. All of the mothers had symptoms during their pregnancies - such as fever and rash - that were consistent with Zika infections. Testing on spinal fluid from seven of the infants was positive for Zika antibodies.
The researchers did CT scans when the babies were between three days and five months old. All showed signs of brain calcification, which is suggestive of brain inflammation.
Many of the babies had other abnormalities, including brain swelling, disruptions in brain folds, underdeveloped brain structures and abnormalities in myelin, which forms protective sheaths on nerve fibres.
Researchers said the findings were consistent with a study published last month testing lab dishes full of nerve stem cells similar to those in the brains of human foetuses. They showed that the Zika virus was able to easily infect these cells, stunting their growth.
Researchers said evidence from the brain scans suggests the abnormalities occurred from a disruption of brain development, rather than a destruction of brain cells.