Mucosal immunity of Indian Antarctic personnel was analysed during the 34th Indian Scientific Expedition to Antarctica (ISEA) by ship voyage. Serum and salivary IgA, IgA1 and IgA2 levels along with salivary cortisol and TGF-β were quantified by enzyme-linked immunosorbent assay. Samples were collected at three different time points (T1, T2 and T3) during the expedition. Serum and salivary IgA, IgA1 and IgA2 concentrations incrementally increased towards the end of the expedition as compared to the beginning of the expedition. Salivary IgA and TGF-β levels were significantly altered during the expedition. Levels of IgA1 (P = 0.0007) and IgA2 (P = 0.0135) increased significantly at T3 as compared to T1. Additionally, significant changes in serum IgA were observed, with peak levels at T3 (P = 0.0015) and T2 (P < 0.001). However, the level of serum IgA2 was also significantly altered at T3 (P < 0.05) and T2 (P = 0.0006) in comparison with T1. The exact cause of the changes in serum and salivary IgA, IgA1, IgA2 and TGF-β levels during the summer expedition are unknown; however, the changes are evident in mucosal immunity.