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The antimicrobial activity of 1,3-disubstituted-1H-naphtho[1,2-e][1,3]oxazines was correlated with their physicochemical parameters using Hansch analysis for first time. The QSAR models were developed by both linear and multiple linear regression and the developed models were cross validated by the “leave one out” technique. The QSAR studies indicated that the antibacterial activity of synthesized compounds was governed by topological parameters, Balaban index (J), Kier's second order molecular index (κα2) and third order molecular connectivity index (3χ) and the antifungal activity was governed by valance first order molecular connectivity index (1χv). The practical applicability of developed models was explored by the design of new compounds based on the information derived from the developed equations.