On the basis of calculations using the density functional theory, it is shown that BNNT synthesis could produce tubes deprived of one (B1 hole) or two (132 hole) boron atoms under the condition where nitrogen atoms exist in excess throughout this study. The relative populations of various isomers of defective tubes will depend on the chirality of the tube. Interestingly, calculations show that B2 holes are much more favored than B1 holes, particularly in armchair tubes. Electronic properties are modified in such a way that the band gap is decreased through the introduction of defect states inside the gap. Magnetic properties will also be dependent on the chirality. The majority of armchair tubes with B2 holes will be nonmagnetic, while the majority of zigzag tubes with defects will exhibit magnetism. Contrary to the case of defect-free BNNT, the defective tubes are expected to be easily subject to reduction by accommodating excess electrons in the presence of Li atoms. In addition, the defect sites will show a higher affinity toward hydrogenation than the defect-free sites.