Abstract Background The implementation of combination antiretroviral therapy (cART) for treating human immunodeficiency virus (HIV) has significantly reduced the rates of vertical HIV transmission. With increasing cART coverage, the number of HIV-positive infants has declined, while the number of HIV-exposed uninfected (HEU) infants has risen. This group now comprises a rapidly expanding cohort of HIV-affected individuals, currently totaling 16 million and increasing by 1.6 million annually. However, our understanding of the potential in-utero toxicity of cART remains limited. Numerous studies, primarily from Africa, suggest that HEU children may face heightened risks of adverse health outcomes, including growth restriction, increased susceptibility to infections, and neurobehavioral disorders. It is widely recognized that infants with growth restriction are at a greater risk of developing chronic diseases such as cardiometabolic and neurological disorders later in life, which is accentuated by low socioeconomic status. The objective of this study was to assess the prevalence of neurodevelopmental disorders and hyperlipidemia in HIV-negative children born to HIV-infected mothers in the Bronx, New York, utilizing retrospective medical records information. Methods We conducted a retrospective chart review of HEU and age-matched control (HIV-unexposed and uninfected; HUU) children (age 0-15 years) using clinical data obtained from the electronic medical record (EMR) at the Montefiore Medical Center in the Bronx, New York, between 2015 and 2023. Demographic data and documented diagnostic data were collected. Lipid panel results were also obtained from the EMR and stratified by age and testing date. Neurodevelopmental outcome measures were compared between HEU and HUU children using Chi-square and Student’s t-test was used for continuous variables. Results A total of 127 HEU (46% females, 54% males) children and 157 HUU (46% females, 54% males) children were analyzed. Among the HEU children, 12 (9.5%) were diagnosed with attention-deficit/hyperactivity disorder (ADHD), while only 1 out of 157 (0.6%) HUU children had this diagnosis (p=0.0004). Similarly, a significant number of HEU children were found to have autism spectrum disorder, with 11 (8.7%) affected compared to 2 (1.3%) in the control group (p=0.0036). HEU children also exhibited a higher prevalence of unspecified developmental delay compared to HUU children (14.2% vs 5.1%; p=0.012). However, no significant differences were observed between the two groups regarding speech and language delay or learning difficulties. Abnormal cholesterol levels were detected in 33% of HEU children, while 54.5% had abnormal triglyceride levels. These percentages surpass the prevalence of pediatric hypercholesterolemia (7%) and hypertriglyceridemia (10.2%) in the United States. Conclusions Our findings indicate that HEU children born in areas designated as medically underserved and socioeconomically disadvantaged, such as the Bronx in the United States, face significant risks of neurodevelopmental disorders and hyperlipidemia. Considering the increasing population of HEU children, even minor rises in adverse health effects could lead to significant public health challenges. To support HEU children in achieving their utmost potential, further studies must be encouraged to understand these children's needs. Moreover, it is imperative to enact policies that facilitate equitable distribution of resources, ensuring timely screening and intervention in underprivileged communities.