Metabolic profiles were detected in healthy and flacherie (inoculated with Bacillus sp.) and grasserie (inoculated with polyhedral bodies)-diseased Bombyx mori larvae. Free amino acids were separated and quantitatively determined by using hydrolysis method. Further, nitrogen (N) percentage was estimated with micro-Kieldahl method. Whereas, phosphor-molybdate method was applied for phosphorus (P) analysis. Results revealed that distinct differences in the amounts of eighteen individual amino acids in healthy and diseased silkworm 5 th larval instar were found. The highest amino acids concentration was recorded in healthy larvae (224.05 mg/g tissue), while the lowest concentration was found in Gr-diseased larvae (177.77 mg/g tissue). Fl-diseased larvae inoculated with Bacillus sp. showed elevation in certain amino acids comparing with Gr-diseased larvae inoculated with of Nuclear Polyhedrosis Virus (NPV) occluded bodies. N and P percentages in Fl and Gr diseases recorded (N = 2.57%, P = 0.29%), (N = 3.86%, P = 0.32%) respectively, compared with healthy larvae (N = 1.63%, P = 0.23%). The present study reveals that a decrease in amino acids in fifth-larval stage implies an increase in N and P percentages in both bacterial and viral infected larvae. It is concluded that the determination of biochemical responses in silkworm against infections may be considered as bio-analytical markers, which are useful for early disease diagnosis and developing disease resistant breeds.