Contiguous gene syndromes (CGS) arise from microdeletions and other aberrations of a chromosome region containing several gene loci. One of the CGSs is Xp21 contiguous gene deletion syndrome (Xp21.3—p21.2) (Xp21 deletion syndrome). Slightly more than 100 male patients suffering from Xp21 contiguous gene deletion have been described in the world literature. This article describes a clinical case of a boy with Xp21 deletion syndrome. Chromosomal microarray analysis revealed a microdeletion of the X chromosome region from position 28085320 to position 33391678 with a size of 5306358 bp, including 11 genes in the imbalance region. The illness declared itself in the neonatal period and manifested early and rapidly as primary adrenal insufficiency (PAI) on the first and second days after birth, with severe metabolic disorders. At 2 years and 7 months, an increase in transaminases was detected for the first time due to metabolic disorders caused by PAI, which led to a misdiagnosis of autoimmune hepatitis. At 2 years and 10 months, the signs of myopathic syndrome were noted, and primary muscular dystrophy was diagnosed. The patient had a pronounced psychomotor development delay from an early age. The child’s mother was diagnosed with the same mutation, including 11 genes in the imbalance region. The hereditary history showed the death of the first boy in the family due to PAI at the age of 6 weeks, which should have been the reason for a comprehensive assessment of the clinical situation and timely medical and genetic counseling to prevent the birth of a sick child from subsequent pregnancies.