Here we consider the initial-boundary value problems in a homogeneous cylindrical domain YI Ω ×+ ( Ω+ is an open two-dimensional bounded simply connected domain with a boundary 5 ∂Ω ∈C , 2 \ Ω≡ Ω − + R is the open exterior of the domain Ω+ , [0, ] YI ≡ Y is the height of the cylinder) on a time interval [0, ] TI ≡ T . The initial conditions and the boundary conditions on the bases of the cylinder are zero, and the boundary conditions on the lateral surface of the cylinder are given by the function 1 2 wx x yt ( , , ,) ( 1 2 (, ) x x ∈∂Ω , Y y ∈ I , T t I ∈ ). An approximate solution of such problems is obtained through the combined use of the Fourier method and the collocation boundary element method based on piecewise quadratic interpolation (PQI). The solution to the problem in the cylinder is expanded in a Fourier series in terms of eigenfunctions of the operator 2 By yy ≡ ∂ with the corresponding zero boundary conditions. The coefficients of such a Fourier series are solutions of problems for two-dimensional heat equations 2 2 t ∇ =∂ + u u ku . With a low smoothness of the functions w in the variable y, the weight of solutions at large values of k increases and the accuracy of solving the problem in the cylinder decreases. To maintain accuracy on a uniform grid, the step of discretization of the boundary function w with respect to the variable y is decreased by a factor of j. Here j is an averaged value of the quantity Y k π depending on the function w. In addition, the steps of discretization of functions ( ) 2 exp − τ k with respect to the variable τ in domains τ≤πT k are reduced by a factor of 2 2 k π . The steps in the remaining ranges of values τ and the steps by the other variables remain unchanged. The approximate solutions obtained on the basis of this procedure converge stably to exact solutions in the 2 ( ) LI I Y T × -norm with a cubic velocity uniformly with respect to sets of functions w, bounded by norm of functions with low smoothness in the variable y, uniformly along the length of the generatrix of the cylinder Y , and uniformly in the domain Ω . The latter is also associated with the use of PQI along the curve ∂Ω over the variable 2 2 ρ≡ − r d , which is carried out at small values of r ( d and r are the distances from the observed point of the domain Ω to the boundary ∂Ω and to the current point of integration along ∂Ω , respectively). The theoretical conclusions are confirmed by the results of the numerical solution of the problem in a circular cylinder, where the dependence of the boundary functions w on y is given by the normalized eigenfunctions of the differential operator By which vary in a sufficiently large range of values of k .