This study was conducted to describe the morphology of tunica mucosa of jejunum and cecum of swine given probiotics (Lactobacillus casei KE-99) in the drinking water. A total of 27 pigs weaned at 21 days of age crossbred pigs [Landrace × (Large White × Duroc)] of both sex and of the same age (~30 days) with initial weight of 7 to 10 kg were allocated in 3 treatment groups and reared for 3 months. The control group (T1) followed the conventional or the recommended farm medication program which included antibiotic (tylosin and zinc bacitracin) in the feeds and without probiotics in drinking water. Treatment 2 (T2) was given 12 g of probiotics mixed with drinking water every other day, while Treatment 3 (T3) was given 12 g of probiotics mixed with drinking water every day. Both T2 and T3 consumed non-medicated feeds. After 3 months, pigs were slaughtered in Animal Science abattoir, College of Agriculture, University of the Philippines Los Baños. After which, the middle part of jejunum and cecum that were about 5 cm long were collected. The results showed that the various morphometric observations (mucosal thickness (µm) and crypt depth (µm) of jejunum and cecum; and villus height (µm), villus width (µm) and villus volume (µm³) of jejunum) on the tunica mucosa of pigs given probiotics supplementation in drinking water (T2 and T3) did not differ significantly from those antibiotic supplemented pigs (T1).