Takayasu arteritis (TAK) is a rare type of large and medial vessel systemic vasculitis. A variety of factors are thought to play a role in the occurrence and development of TAK such as human leukocyte antigen-B52, autoimmunity, inflammation and environmental factors. 3q29 microdeletion syndrome is also a very rare inherited disease, which includes intellectual disability, growth retardation and neuropsychiatric disorders. Here, we present a case with concomitant TAK and 3q29 microdeletion syndrome. A 22-year-old woman presented to the emergency department with sudden bilateral vision loss and severe headache. During physical examination, the patient was noted to have a difference in blood pressure between extremities. Computed tomography angiography revealed vascular wall inflammation in the abdominal aorta. Based on clinical and radiographical findings, a diagnosis of TAK was made. Concurrently, the patient was found to have short stature and intellectual disability. A possible genetic etiology was sought out. Chromosome analysis showed a 1.5 Mb heterozygous deletion on chromosome 3 and a diagnosis of 3q29 microdeletion was made. Additional imaging also revealed a split cord in medulla spinalis along with hemivertebrae and fusion anomalies, neither of which were reported in TAK or 3q29 microdeletion cases in the literature.