This paper presents the results of the studies on detection of fruit bruises and watercore in their tissues. Both passive and active pulse phase thermography was applied to early detect tissue defect. Watercore occurrence in ‘Gloster’ apples was evaluated from heating curves. It was found that the derivative of apple temperature in time per apple mass is a good parameter to identify apples with and without watercore. For apples with water-core the rates of temperature increase per mass in particular initial stages of heating were considerably lower than for apples without watercore affected tissue irrespective of the part of the fruit surface from which the measurements were made. Pulsed-phase thermography (PPT) method was used to detect early apple bruises in ‘Idared’ and ‘Gloster’. In PPT method the studied object is heated with an individual thermal pulse (most frequently a rectangular pulse) and the temperature decay on the surface is analysed on a pixel by pixel basis as a mixture of harmonic waves, thus enabling the computation of phase and amplitude images. The analysis of phasegrams made it possible to determine the relation between the frequency response, phase delay and defect depth. PPT method used for early bruise detection enables identify defects which are invisible in passive thermography.