This paper presents some recent advances in the boundary element method (BEM) for the analysis of carbon nanotube (CNT)-based composites. Carbon nanotubes, formed conceptually by rolling thin graphite sheets, have been found to be extremely stiff, strong and resilient, and therefore may be ideal for reinforcing composite materials. However, the thin cylindrical shape of the CNTs presents great challenges to any computational method when these thin shell-like CNTs are embedded in a matrix material. The BEM, based on exactly the same boundary integral equation (BIE) formulation developed by Rizzo some forty years ago, turns out to be an ideal numerical tool for such simulations using continuum mechanics. Modeling issues regarding model selections, representative volume elements, interface conditions and others, will be discussed in this paper. Methods for dealing with nearly-singular integrals which arise in the BEM analysis of thin or layered materials and are crucial for the accuracy of such analyses will be reviewed. Numerical examples using the BEM and compared with the finite element method (FEM) will be presented to demonstrate the efficiency and accuracy of the BEM in analyzing the CNT-reinforced composites.