Chromosome aberrations or genetic syndromes associated with cloacal-bladder exstrophy complex have rarely been reported. The aim of this report is to describe a 14 year-old female Brazilian patient with a complex urogenital malformation, short stature, lack of secondary sexual characteristics and Y chromosome aberration. A girl with cloacal bladder exstrophy complex was referred for evaluation of short stature and absence of secondary sexual characteristics. Pre-pubertal levels of gonadotropins and sex steroids were observed at the beginning of monitoring, but follow-up showed a progressive increase in testosterone levels. The patient underwent gonadectomy and testicular tissue was identified without dysgenetic characteristics. She had a 46,X,inv(Y)(p11.1q11.2) karyotype, normal SRY sequence, and no Y deletions. The pericentric inversion of Y chromosome apparently did not contribute to the development of the complex urogenital malformation in this patient. Currently, no teratogenic agent, environmental factor, or defective genes have been recognized as etiologic factors for this type of urogenital malformation.