The present study describes the in vivo ameliorating effect of Lactobacillus casei supplementation in renourished Giardia intestinalis infected BALB/c mice. It was observed that daily administration of probiotic 7 days prior to Giardia-infection to renourished mice, efficiently reduced the excretion of Giardia cysts and trophozoite counts, along with significant increased fecal lactobacilli counts compared with Giardia-infected mice. It was also observed that oral feeding of probiotic to renourished-Giardia-infected mice abrogated all the anthropometric and biochemical anomalies. Histologically, morphological and cellular alteration of microvillus membrane integrity revealed that probiotic administration further ameliorated the mucosal damage in renourished-probiotic-Giardia-infected mice compared to severe microvillus atrophy, oedematous, vacuolated epithelial cells and ileitis in renourished-Giardia and Giardia-infected mice. Thus, it is suggested that probiotic used as the functional food helps in restoration of anthropometric, biochemical alterations and atrophied gut by enhancing the goblet cells and reducing the giardiasis.