This article presents the operation of an automatic pine sawn timber inspection system, which was developed at the Woodinspector company and is offered commercially. The vision inspection system is used to detect various wood defects, including knots, blue stain, and mechanical damage caused by worms. A blue stain is a defect that is difficult to detect based on the color of the wood, because it can be easily confused with wood defects or dirt that do not impair its strength properties. In particular, the issues of detecting blue stain in wood, the use of artificial neural networks, and improving the operation of the system in production conditions are discussed in this article. While training the network, 400 boards, 4 m long, and their cross-sections of 100 × 25 [mm] were used and photographed using special scanners with laser illuminators from four sides. The test stages were carried out during an 8-hour workday at a sawmill (8224 m of material was scanned) on material with an average of 10% blue stain (every 10th board has more than 30% of its length stained blue). The final learning error was assessed based on defective boards detected by humans after the automatic selection stage. The system error for 5387 boards, 550 m long, which had blue staining that was not detected by the scanner (clean) was 0.4% (25 pieces from 5387), and 0.1 % in the case of 3412 boards, 610 mm long, on which there were no blue stains, but were wrongly classified (blue stain). For 6491 finger-joint boards (180–400 mm), 48 pieces were classified as class 1 (clean), but had a blue stain (48/6491 = 0.7%), and 28 pieces did not have a blue stain, but were classified as class 2 (28/3561 = 0.7%).