Vismodegib is an effective treatment for advanced basal cell carcinoma (BCC), but primary resistance to vismodegib remains to be elucidated. Alternative approaches may be warranted to help better select patients who are most likely to be responsive to treatment. The identification of immuno-histochemical markers may support this perspective, as well as a better understanding of resistance mechanisms. To determine the level of expression of CD56, PDGF-Rα, CD117, MMP9, TIMP3, and CXCR4 in advanced BCC, and explore whether expression levels are associated with a lack of response to vismodegib. A cross-sectional study was conducted. Immuno-histochemical markers were selected based on their roles in tumour proliferation and/or migration in BCC or skin tumours. Expression was evaluated on a 5-point scale. Tissue samples included were pre-treatment advanced BCC samples from patients treated with vismodegib, with an available response after six months of treatment. Regression optimised models were used to build hypotheses regarding a possible association between expression levels and a lack of response to vismodegib, which was then tested by logistic regression. Twenty-three patients were included. The percentage of samples expressing markers ranged from 43.5% for CD117 to 91.3% for CXCR4. CD56 expression was significantly associated with an increased risk of lack of response to vismodegib (OR = 5.5; CI 95%: 3.4-29.8; p = 0.0488); a similar association was suggested for CXCR4 (p = 0.066), but not identified for other markers. These results provide us with a better understanding of the expression of immuno-histochemical markers in advanced BCC. A further detailed analysis of CD56 expression may provide insights into guiding further investigation of the correlation between this marker and a lack of response to vismodegib.