Although primary cutaneous neuroendocrine cell carcinoma [Merkel cell carcinoma (MCC)] may show divergent features, including microcystic ('tubuloglandular'), squamous, eccrine and rhabdomyoblastic, a diffuse microcystic pattern is exceedingly rare. In this study, we present two cases of MCC with prominent microcystic features, which precluded a definitive diagnosis in the initial punch biopsy. Both patients were middle-aged men with a history of rapidly growing plaques of the back or posterior neck. Punch biopsies from both patients revealed an infiltrating neoplasm with prominent microcystic features that mimick tubuloglandular structures, lined by hyperchromatic basaloid cells, which were strongly positive for chromogranin and BerEP4, variably positive for CK7 and CK5/6 and negative for CK20, synaptophysin, S-100, epithelial membrane antigen (EMA), gross cystic disease fluid protein-15 (GCDFP-15), estrogen/progesterone receptors (ER/PR), thyroid transcription factor 1 (TTF1) and carcinoembryonic antigen (CEA). The re-excision specimens showed a multifocal intra-epidermal component in one case and typical finely stippled nuclear chromatin in both cases. Although the lack of CK20 staining is unusual, the histologic characteristics along with the remaining immunohistochemical studies favor the diagnosis of a primary cutaneous neuroendocrine cell carcinoma over the variants of eccrine carcinoma or basal cell carcinoma with neuroendocrine differentiation. Our cases illustrate that prominent microcystic features, mimicking glandular differentiation, may occur in MCC and pose a diagnostic challenge in small biopsy specimens.