The aim of this study was to investigate the root canal configuration, accessory canals and number of main foramina of 123 maxillary second molars by means of micro-computed tomography. The teeth were scanned and reproduced with 3D software imaging. The root canal configuration and number of main foramina were evaluated by means of a four-digit system. The morphological complexity of human maxillary second molars is depicted by the number of accessory and connecting canals. The most frequently observed root canal configurations in the mesiobuccal root were 2-2-2/2 (19.5%), 2-2-1/1 (14.6%) and 2-1-1/1 (13.0%). A 1-1-1/1 configuration was observed in 93.5% and in 96.7%in the distobuccal and palatal roots, respectively. The MB1 root canal had one accessory canal (18.7%), and 8.9%of the MB2 root canal had one or two accessory canals. The distobuccal (11.3%) and palatal (14.6%) root canals had at least one accessory canal, and connecting canals were observed in 16.3% of mesiobuccal roots. The MB1, MB2, distobuccal and palatal root canals had one main foramen in 99.2%, 43.1%, 98.4% and 99.2% of samples, respectively. In the mesiobuccal root, one accessory foramen was detected in 14.6%, two were detected in 7.3%, and three were detected in 5.7%. The distobuccal root showed one or two accessory foramina in 9.1%of samples. The root canal configuration of maxillary second molars is quite heterogeneous; the mesiobuccal root has predominantly two root canal entrances (58.4%, 1 in 41.1%) with one main foramen (54.4%). Two main foramina were observed in 43.0%. Morphological variations, connecting and accessory canals were observed in all apical thirds.