Background: Elevation of pro-inflammatory cytokines has been reported in patients with vitiligo and metabolic syndrome (MetS) standalone. However, the role of these cytokines in comorbid vitiligo and MetS is not known. Methods: This study evaluated serum cytokines (innate immunity, Th1, Th2, and Th17) and high sensitivity C-reactive protein (Hs-CRP) in patients with vitiligo (n = 75) and controls (n = 100) with and without MetS. The ratio of innate cytokines to Th1, Th2, and Th17 cytokines was evaluated in vitiligo patients with (Group 1) and without MetS (Group 2) and controls with (Group 3) and without MetS (Group 4), respectively. The ability of cytokines to discriminate patients with MetS from those without was evaluated by area under the receiver operating characteristic curve. Results: Patients with MetS (vitiligo and controls) had significantly (analysis of variance, P < 0.001) higher levels of cytokines released from innate cells (interleukin [IL]-1 alpha, IL-1 beta, IL-6, IL-8, IL-12, IL-15, and tumor necrosis factor-alpha) as compared to patients without MetS. The ratio of innate cytokines to Th1, Th2, and Th17 cytokines was significantly higher in vitiligo patients with MetS compared to subgroups without MetS. The significantly greater area under the receiver operating curve (area under the curve = 0.948) for innate immunity cytokines indicated that innate immunity cytokines had a higher discriminatory ability to differentiate MetS patients as compared to other cytokines (Th1, Th2, and Th17). Conclusion: Comorbid vitiligo and MetS have cytokine imbalance and significantly higher levels of pro-inflammatory cytokines. Vitiligo patients having innate cytokine levels above 6.14 pg/mL and Hs-CRP levels above 6.5 are more likely to develop MetS.