Background: Microcystic adnexal tumor is a rare sclerosing variant of ductal carcinoma of eccrine sweat glands which is highly invasive. This tumor is often misdiagnosed as other benign or malignant skin lesions and improper treatment is carried on and is associated with high recurrence rate. Case presentation: We reported here in a 59-years old man who underwent incisional biopsy for a ongenital lesion on posterior neck which had grown recently. Microscopic examination exhibited an infiltrative tumor as constituted by small cord-like and angulated tubules with tadpole or comma-like shapes, individually set in abundant fibrous stroma in dermis. So, the diagnosis was syringoma. In the next step, the lesion underwent excisional biopsy. Histologically, a tumor located in dermis with extension to subcutis was noted which contained basaloid keratinocytes with occasional horn cysts and abortive hair follicles. In other areas, ducts and gland-like structures lined by two-cell layers predominated. The tumor extended to skeletal muscle and perineurial structures but no significant atypia or mitosis was identified. Eventually, with respect to mentioned features, the diagnosis was microcystic adnexal tumor. Conclusion: It is concluded that thinking about this rare invasive skin tumor with proper use of Mohs’ surgery and its correct diagnosis is clinically of high significance to reduce its recurrence rate. Meanwhile, this tumor was noticeably set in a congenital lesion in this reported case.