Vitamin D dependent rickets is a rare autosomal recessive disorder secondary to mutation in 1 α hydroxylase enzyme gene. We are presenting a case of a two-year-old boy with vitamin D dependent rickets type 1A whose diagnosis was missed for a long period and he was treated as nutritional rickets. He suffered with severe hypotonia and regressing milestones. Severe hypotonia with proximal muscle weakness caused respiratory failure which required intensive care admission and mechanical ventilation. DNA analysis revealed previously reported homozygous mutation in CYP27B1 gene (p.Arg429Pro (R429P) at exon c.1286 G > C). Rare genetic disorders of rickets are not considered in early course of disease in regions with high prevalence of vitamin D deficiency. This severe presentation of rickets highlights the need of close monitoring of treatment response and consideration of other differential diagnosis in children who are not responding to vitamin D supplements. There is a high prevalence of genetic disorders particularly autosomal recessive conditions in societies having high rate of inter-family and consanguineous marriages.