Interstitial deletions in the long arm of chromosome 3, although relatively rare, have previously been reported to be associated with several congenital anomalies and developmental delays. Around 11 individuals with interstitial deletion spanning the region 3q21 were reported to have overlapping phenotypes, including craniofacial dysmorphism, global developmental delay, skeletal manifestations, hypotonia, ophthalmological abnormalities, brain anomalies (mainly agenesis of corpus callosum), genitourinary tract anomalies, failure to thrive and microcephaly. We present a male individual from Kuwait with a 5.438 Mb interstitial deletion of the long arm of chromosome 3 (3q21.1q21.3) detected on the chromosomal microarray with previously unreported features, including feeding difficulties, gastroesophageal reflux, hypospadias, abdomino-scrotal hydrocele, chronic kidney disease, transaminitis, hypercalcemia, hypoglycemia, recurrent infections, inguinal hernia and cutis marmorata. Our report expands the phenotype associated with 3q21.1q21.3 while summarizing the cytogenetics and clinical data of the previously reported individuals with interstitial deletions involving 3q21, thus providing a comprehensive phenotypic summary.