This study profiled microbes present in the cerebrospinal fluid (CSF) of pediatric patients with infectious and non-infectious hydrocephalus. 92 children from Uganda, including 58 with postinfectious hydrocephalus (PIH) and 34 with non-postinfectious hydrocephalus (NPIH). 92 cerebrospinal fluid (CSF) samples retained in this workflow; V1-V2 region of 16S rRNA gene. Case-control (retrospective) design with samples collected in the first ~100 days of life.