OBJECTIVE The aim of the present study was to perform a retrospective review of the lesion sites in congenital middle-ear cholesteatoma and any accompanying ossicular defects, as well as to explore the possible aetiology of congenital middle-ear cholesteatoma associated with such ossicular chain defects. METHODS The clinical characteristics and pathogenic mechanisms of ossicular chain defects were investigated in 10 patients with early-stage congenital middle-ear cholesteatoma confirmed by surgery, from August 2011 to February 2019. RESULTS Monofocal cholesteatoma was located in the anterosuperior quadrant in 3 cases and in the posterosuperior quadrant in 7 cases; all 10 cases showed an absence of the long crus of incus, and 8 cases showed a complete or partial absence of stapes superstructure. The lesions were confined to the vestibular window and the stapes region and had no contact with the long crus of the incus or stapes in nine cases. None of the 10 patients had any recurrence of cholesteatoma. CONCLUSIONS Although cholesteatoma can cause erosion of ossicles, the present cases suggest that residual epithelium of the cholesteatoma may coexist with ossicular malformations. Therefore, the aetiology of the clinical characteristics in these patients may derive from residual epithelial hinderance of ossicle development.