Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV) and characterized by progressive failure of the immune defense resulting in life threatening complications such as infections and cancers. Perinatal transmission during pregnancy is the frequent mode of HIV-infection in children, and is shown to associated with increased risk of mortality and developmental delay¹. The impact of HIV-infection on a child’s neurodevelopment extends beyond the direct effect of the HIV on the central nervous system² (CNS). Studies based on neurological symptoms suggest that HIV CNS involvement can occur well before the first AIDS defining illness in as many as 18% of pediatric patients. HIV-related encephalopathy can be observed as static or progressive with microcephaly, delay in normal development and pyramidal tract symptoms³. Various histological and neuroimaging studies have demonstrated brain tissue injury in multiple brain sites in cortical and subcortical areas in adolescent and adult HIV-infected patients and found correlations between brain tissue loss, cognitive and motor impairments and CD4+ counts^4,5. Though different neuroimaging studies investigated structural brain changes in adolescent and adult HIV the regional cortical thickness and subcortical volume changes and structural brain connectivity are not yet studied in perinatally HIV-infected children.The purpose of this study to evaluate the cortical and subcortical changes and alteration in structural connectivity in perinatally HIV-infected children compared to those of healthy volunteers.Fifty-nine HIV-seropositive (age=10±2.3 years) children’s and 28 HIV-seronegative controls of similar demographics were included in this study. HIV-infection was confirmed by enzyme-linked immunosorbent assay and western blot analysis. Institutional Ethical Committee approved the protocol and informed consent was obtained in subjects. All subjects underwent brain magnetic resonance imaging (MRI) at 3T clinical MR Scanner (GE Healthcare Technologies, Milwaukee, WI, United States) using a standard quadrature head coil. Conventional T2-, T1-weighted and FLAIR imaging and a high-resolution T1-weighted structural imaging using a fast spoiled gradient echo BRAVO pulse sequence (TR=8.4 ms; TE=3.32 ms; inversion time=400 ms; FA=13°; matrix size=512×512; FOV=240×240 mm²; slice-thickness =1.0 mm) was performed on each subject. T2-, T1-weighted and FLAIR images were examined for any gross brain pathology, such as cysts, tumors, or any other mass lesions, and presence of such anomaly was used as an exclusion criteria. High-resolution T1-weighted images were used for measuring regional cortical thicknesses and subcortical volumes in HIV and control subjects using FreeSurfer (v. 5.3.0), as described in details elsewhere⁶. Regional changes in cortical and subcortical structures between HIV-seropositive and HIV-seronegative control subjects were examined from both left and right hemisphere separately using a vertex-by-vertex general linear model, implemented in FreeSurfer (age and gender as covariates, p <0.05; using FDR, correction for multiple comparisons). For the strctural networks construction we used graph theory based analysis using GAT software that used the freesurfer derived metrix described in details elsewhere⁷.All the statistical computations were performed using the Statistical Package for Social Sciences version 16.0. Pearson correlations between CD4+ counts and neuropsychological test scores with cortical and subcortical structures were performed. A p-value of less than 0.05 was considered to be statistically significant.15 HIV-seropositive children’s showed hyper-intensity on T2-weighted and FLAIR images and 1 patient showed motion artifact were excluded from analyses. HIV-seropositive children showed significant change in both cortical thickness (figure 1) and subcortical volumes (table 1), as well as week correlation matrix and reduced brain structural connectivity (figure 2) in both left and right hemispheres compared to those of HIV-seronegative controls. CD4+ counts and neuropsychological scores significantly correlated with changes in cortical and subcortical structures both in left and right hemispheres in HIV-seropositive children.We observed cortical and subcortical atrophy as well as hypertrophy and altered structural brain connectivity in HIV-seropositive children, suggesting presence of brain tissue injury in multiple brain sites in these patients, which is consistent with the previous study in HIV-seropositive youth⁴. These multiple brain sites are involved in regulating various functions including cognitive, visual, sensory and motor functions. Our findings suggest that the presence of widespread changes that includes both cortical and subcortical structures may indicate early developmental cerebral injury in perinatally infected HIV-seropositive children. Altered brain connectivity in HIV-seropositive children compared to HIV-seronegative children suggests abnormality in structural and neuronal connectivity, which may be the reason for abnormal neuropsychological scores in HIV-seropositive children. Pathophysiological mechanism of brain tissue injury may include ongoing HIV-infection resulting inflammation in brain and subsequently neuronal tissue injury. The cortical thickness and subcortical volumes and structural networks connectivity measurements may provide an early biomarker of HIV-related brain tissue injury in HIV-seropositive children.