This study was designed to check the dietary effect of different levels of lysine on intestinal morphology, cecal tonsils and goblet cell count in Japanese Quails. For this Purpose, a total of 100, day old chicks were randomly divided in four groups. These groups were further sub-divided into five replicas per group, each replica having five birds. NRC has recommended 13g/kg of lysine in basal diet in 1994. The birds of control group (first) were fed with basal diet containing 13 g/kg of lysine, second experimental groups fed contained lysine at the rate of 11.7g/kg of lysine, third group 13.6 g/kg of lysine and fourth group 14.9 g/kg, respectively for 35 days. The results showed a significant increase (P<0.05) in villus height (VH), villus width (VW), villus surface area (VSA) and muscular mucosa thickness (MMT) in all parts of the small intestine of 13.65 g/kg supplemented birds. In jejunum, VH, VW, VSA, lamina propria thickness (LPT) and MMT was increased at levels 13.65 g/kg and 14.95 g/kg. Crypt depth (CD) and muscularis externa thickness (MET) did not vary in both duodenum and jejunum, in ileum CD and MET was increased (P<0.005) in treated groups 13.65 g/kg and 14.95 g/kg. LPT was increased (P<0.005) in duodenum and jejunum, while in ileum it was insignificant. Total goblet cells count was increased in all duodenum, jejunum and ileum. In duodenum acidic mucin and total GC count was significant (P<0.005) in lysine treated groups at 13.65 g/kg and 11.7 g/kg level while mixed mucin GC count was non-significant. In jejunum and ileum portion acidic mucin, mixed and total GC count was higher (P<0.005) in 13.65 g/kg group. In cecal tonsils length, width, area and number of lymphatic nodule and was significant (P<0.005) in 13.65 g/kg. Lysine supplementation of 13.65 g/kg is beneficial feed additive for Japanese Quails on intestinal morphology.