Background: Warts constitute the commonest cutaneous manifestation of human papillomavirus (HPV) infection. Intralesional Candida antigen immunotherapy is used for wart treatment especially with resistant cases. Objective: To detect the association between different HPV genotypes, level of induced protein 10 (IP-10) and the clinical response to Candida antigen immunotherapy. Methodology: A cross-section study was conducted on 57 patients with resistant warts. All patients were injected with Candida antigen intralesionally at 2-weeks intervals for six treatment sessions. Clinical response was evaluated after 6 sessions. HPV genotyping was performed using real time PCR. Whole blood from patients was incubated with Candida antigen and IP-10 level was measured by ELISA. Results: Among the 57 injected patients, 31 (54.4%), 18 (31.6%), 8 (14%) show complete, partial and no response respectively. The most frequently detected genotype was HPV-39 (7.1 %) from HPV positive samples. Viral genotype had no significant relation (P=0.305) with patients' clinical response. Statistically significant different IP-10 levels (P<0.001) were detected with different clinical responses. In conclusion: HPV genotype has no significant relation with the clinical response to Candida antigen immunotherapy in wart patients. IP-10 level is an excellent predictive factor for the immune response and hence for the clinical response in those patients.