An adjoint-based method is presented for determining manufacturing tolerances for aerodynamic surfaces with natural laminar flow subjected to wavy excrescences. The growth of convective unstable disturbances is computed by solving Euler, boundary layer, and parabolized stability equations. The gradient of the kinetic energy of disturbances in the boundary layer (E) with respect to surface grid points is calculated by solving adjoints of the governing equations. The accuracy of approximations of ΔE\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Delta E$$\\end{document}, using gradients obtained from adjoint, is investigated for several waviness heights. It is also shown how second-order derivatives increase the accuracy of approximations of ΔE\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Delta E$$\\end{document} when surface deformations are large. Then, for specific flight conditions, using the steepest ascent and the sequential least squares programming methodologies, the waviness profile with minimum L2-\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$L2-$$\\end{document}norm that causes a specific increase in the maximum value of N- factor, ΔN\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Delta N$$\\end{document}, is found. Finally, numerical tests are performed using the NLF(2)-0415 airfoil to specify tolerance levels for ΔN\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Delta {N}$$\\end{document} up to 2.0 for different flight conditions. Most simulations are carried out for a Mach number and angle of attack equal to 0.5 and 1.25∘\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$1.25^{\\circ }$$\\end{document}, respectively, and with Reynolds numbers between 9×106\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$9\ imes 10^6$$\\end{document} and 15×106\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$15\ imes 10^6$$\\end{document} and for waviness profiles with different ranges of wavelengths. Finally, some additional studies are presented for different angles of attack and Mach numbers to show their effects on the computed tolerances.Graphic abstract