Higher haplotype carrier frequencies of HLA-DRB1*04:01-DQB1*03:01 (P = 2.88 × 10–5, OR 7.32, 95% CI 2.85‒18.81) and DRB1*09:01-DQB1*03:03 (P = 0.0090, OR 1.84, 95% CI 1.19‒2.86) and lower DRB1*13:02-DQB1*06:04 (P = 0.0050, OR 0.26, 95% CI 0.09‒0.73) were found in MCTD patients than in controls. Here, HLA-DRB1 is linked to mixed connective tissue disease.