The contribution of natural wood defects such as knots is an important factor influencing the strength characteristics of structural timber. This paper discusses the use of active thermography in the timber diagnostics, particularly in the determination of the knot area ratio (KAR) in elements covered with paint coatings. Moreover, on the basis of thermal images, the localization for the subsequent semi-destructive tests (SDTs) was established. Three different sources of external energy supply were used in the studies: laboratory dryer, air heater and halogen lamps. The active thermography tests were performed on elements made of three wood species (fir, pine and spruce). The specimens were covered with varying layers of paint coatings and primers, to reflect the actual condition of the historic structural elements. The obtained thermal images enabled the estimation of the KAR, due to the difference in temperature between solid wood and knots occurring therein. It should be noted that the results were affected by an external energy source and subjective judgement of the operator. Moreover, active thermography could be an effective method for the indication of the regions within which SDTs should be performed in order to properly assess the technical state of an element covered with polychrome.