This paper deals with a method for predicting the three-dimensional distribution of internal defects from the two-dimensional observation of intercepted defects on an inspection plane by an inverse analysis. At first, the fundamental relationships between them were analytically derived on the basis of a statistical model where multiple penny-shaped cracks in an infinite body were intercepted by an inspection plane. The validity of the method was confirmed by a numerical simulation. It was, moreover, applied to small creep fatigue cracks distributing in a smooth specimen of a Type 304 stainless steel, and the volumetric density and the distribution of crack size were successfully evaluated.