Follicular hybrid cysts including two or more components of the epithelial skin adnexa are very rare. The epithelial lining of hybrid cysts varies, and either contains epidermis, and trichilemmal squamous epithelium, or other epithelia of the skin adnexa. Hybrid cysts may also be associated with neoplasia, such as in situ carcinoma, Bowen's disease and squamous cell carcinoma. A 37-year-old female was complaining of a cyst on her scalp. The unilocular cystic lesion was lined with markedly atypical squamous cells with trichilemmal differentiation. Marked nuclear and cytological atypia, pleomorphism, numerous mitotic figures and atypical mitosis was detected in the squamous epithelium. The epithelium of the cyst was also composed of ductal structures lined with cuboidal epithelium. Immunohistochemical staining was positive for cytokeratin 7 (CK7) in both squamous and glandular epithelium. Luminal staining was shown by carcinoembryonic antigen (CEA), although gross cystic disease fluid protein-15 (GCDFP-15) was negative in the glandular epithelium. In addition, p16 tumor suppressor gene was strongly positive in both the squamous and glandular epithelium. Overall, the unique cystic lesion reported contained pilar squamous epithelium with in situ carcinoma and eccrine ductal structures, which was interpreted as a hybrid cyst composed of in situ trichilemmal carcinoma and a ductal eccrine component.