Eye drop (ED) and vent brush (VB) application of live infectious laryngotracheitis virus (ILTV) vaccine provides protective immunity against disease, but little is known regarding the immune responses following application. This study compared the gene expression of immune markers associated with VB and ED ILTV vaccination in the conjunctiva, trachea and cloaca at 3, 5, 7 and 10 days post-vaccination (dpv) and 3, 5 and 7 days post-revaccination (dprv). The relative gene expression of markers associated with inflammatory responses and their regulation (CCL4, CCR5, IL2, IL4, IL6, IL17C, IFNG), pathogen recognition receptors (TLR2-2, TLR4, TLR7) and cell surface markers (CD4, CD8A, CD14, CD80) was evaluated by RT-PCR after ED or VB vaccination and revaccination using the alternate route [ED/VB (primary/booster), VB/ED). There was increased expression of inflammatory markers at vaccination sites following primary vaccination. In VB group, there was increased expression of IL6 and IFNG in cloaca (3 dpv) and IL2 in conjunctiva (7 dpv) compared to ED group (P < 0.05), while there was increased CCL4 expression in conjunctiva (5 dpv) in ED group compared to VB group. ED vaccination was associated with increased expression of IL2 and IL17C in trachea while VB vaccination was associated with increased expression of IL6 and IL17C in trachea. Similarly, ED/VB and VB/ED associated increases in IL2, IL6 and IL17C expression were observed in the revaccination sites. In conclusion, immune responses after the first and second ILTV vaccination were site-specific and associated with inflammatory responses in the mucosa of the vaccinated tissues and trachea.