Multiple sulfatase deficiency (MSD) is an ultra-rare lysosomal disease caused by defective activation of cellular sulfatases comprising clinical features of mucopolysaccharidoses, sphingolipidoses, and other sulfatase deficiencies. We present a case of an infant with feeding difficulties related to autism spectrum disorder (ASD) who was diagnosed at 10 months of age with MSD by next-generation sequencing (NGS). Biochemical results obtained in dried blood spot (DBS) samples were inconsistent and not suggesting MSD in the light of identified pathogenic SUMF1 variants. However, follow-up analyses at 20 months of age revealed an increased concentration of sulfatides in DBS. It should be noted that biochemical tests, routinely used as screening methods, have a risk of false negative results, especially regarding mild/attenuated phenotypes, as presented in our report.