In this report, we described an infant with both partial biotinidase and IL-12R beta 1 deficiencies as these two entities are rare and unrelated inherited disorders. One-month-old girl was diagnosed as partial biotinidase deficiency with newborn screening programme. Mutation analysis revealed a compound heterozygous mutation BTD: c.1330G>C (p.Val444Leu) / c.196_197dupCATC (p.Leu69HisfsTer24). At the age of 6 months, a nodule on her left axilla with purulent discharge was noticed which was related to BCG vaccination. A mutational analysis revealed a homozygous c.783+1G>A mutation on IL-12R beta 1 gene. Interferon-gamma and anti-tuberculosis treatment were initiated together and the nodule with purulent discharge regressed dramatically. Here, we want to emphasize consideration of coexistence of two rare autosomal recessively inherited diseases in a patient due to the high rate of consanguinity in our country.