Viral infections during childhood can increase susceptibilities to neurodevelopmental and psychiatric disorders, leading to concerns about the current pandemic. An emerging hypothesis is that some neurological disorders and mental health deficits may stem from gastrointestinal (GI) dysfunction, caused, or worsened by inflammation. Children living in economically disadvantaged areas would be expected to show more GI problems due to decreased access to nutritional foods, which was likely further limited by the pandemic. Recent studies indicate the gut microbiome and its metabolic products regulate behavioral responses through interactions with endocrine, gut, and central nervous system pathways. We can now explore COVID-19’s potential short- and long-term effects on mental health in a newly launched prospective study of children treated at JH Community Physician’s Clinic in Baltimore, MD.