This paper explores an isogeometric boundary element method (IGA-BEM) for sloshing problems in cylindrical tanks with single and multiply connected domains. Instead of the Lagrange basis functions used in the standard BEM, the nonuniform rational B-splines (NURBS) basis functions are introduced to approximate the geometries of the problem boundaries and the unknown variables. Compared with the Lagrange basis functions, NURBS basis functions can accurately reconstruct the geometric boundary of analysis domain with almost no error, and all the data information for NURBS basis functions can be directly obtained from the computer-aided design (cad) or computer-aided engineering (cae) commercial software, which implies the modeling process of IGA-BEM is more simple than that of the standard BEM. NURBS makes it possible for the IGA-BEM to realize the seamless connection between cad and cae software with relative higher calculation accuracy than the standard BEM. Based on the weighted residual method as well as the divergence theorem, the IGA-BEM is developed for the single and multiply connected domains, whose boundaries are separately defined in the parameter space by different knot vectors. The natural sloshing frequencies of the liquid sloshing in a circular cylindrical tank with a coaxial or an off-center circular pipe, an elliptical cylindrical tank with an elliptical pipe, a circular cylindrical tank with multiple pipes are estimated with the introduced method by assuming an ideal (inviscid and incompressible) liquid, irrotational small-amplitude sloshing, and the linear free-surface condition. The comparison between the results obtained by the proposed method and those in the existing literatures shows very good agreements, which verifies the proposed model well. Meanwhile, the effects of radius ratio, liquid depth, number, and location of internal pipe (pipes) on the natural sloshing frequency and sloshing mode are analyzed carefully, and some conclusions are outlined finally.