Here we describe the case of a pig with intersex traits including ambiguous external genitalia, sex chromosome abnormalities and a late-onset vanishing testis-like syndrome. It was identified shortly after birth by presenting a predominantly female phenotype with two large scrotal masses resembling testes. The karyotype is 38,XX (53%)/38,XY (47%). Sex steroid levels were undetectable at 1 and 7 months old, whereas circulating cortisol levels were typical. DNA studies excluded gene alterations in sex-determining region Y (SRY), dosage-sensitive sex reversal-congenital adrenal hypoplasia critical region on the X chromosome protein 1 (DAX1), SRY-related high mobility group-box gene 9 (SOX9), nuclear receptor subfamily 5, group a, member 1 (NR5A1), nuclear receptor subfamily 3, group c, member 4 (NR3C4) and steroid 5-alpha-reductase 2 (SRD5A2). At 8 months of age the XX/XY pig evinced delayed growth; however, the most striking phenotypic change was that the testes-like structures completely vanished in a 2–3-week period. The internal genitalia were found to consist of a portion of a vagina and urethra. No fallopian tubes, uterus or remnants of Wolffian derivatives were observed. More importantly, no testes, ovaries, ovotestis or gonadal streaks could be identified. The XX/XY sex chromosome dosage and/or overexpression of the DAX1 gene on the X chromosome in the presence of a wild-type SRY gene may have caused this predominantly female phenotype. This specimen represents an atypical case of 38,XX/38,XY chimeric, ovotesticular disorder of sex development associated with agonadism.