Mucopolysaccharidosis VI is a lysosomal storage disease with a progressive autosomal recessive inheritance pattern. It is determined by variants in the gene that encodes a lysosomal enzyme, arylsulfatase B, located on chromosome 5 (5q13-5q14). The reduction in enzymatic activity results in the incomplete degradation and intralysosomal accumulation of glycosaminoglycans. The pedigree is considered an important tool in the early identification of patients with hereditary genetic diseases. Herein, we report the case of a 3-year-old female patient of non-consanguineous parents, with a relevant family history of sisters with MPS VI, who died at 7 years of age and a brother who died at 15 days of birth due to unknown causes. At birth, he presented scaphocephaly with frontal prominence, a low nasal bridge, and a full moon face. Due to the family history, an enzymatic and molecular study of the ARSB gene was conducted with a low enzymatic value and pathogenic variant, through which a phenotype-genotype correlation was made in the neonatal stage. In our country, there are no neonatal screening policies for lysosomal storage diseases. In addition, the compromise of the phenotype may be subtle in some newborns, hence the importance of the pedigree and good clinical history for early detection, to establish specific and directed treatments that reduce the morbidity-mortality attributed to these pathologies, follow-up and genetic counselling. This case also provides more information currently available on a disease that is considered for our country as an orphan, approaching personalised precision medicine.