Pile diagnostics, namely the control of integrity and length, is a very urgent task both during the construction of buildings and structures and during their inspection. Regular conditions for control are the availability of free access to the pile head. However, in many cases, the task is complicated by the presence of a cap on piles. This significantly complicates not only the technology for measuring by Pulse Echo Method and the Transient Response Method, but also the process of received signal processing. The data obtained by numerical modeling and field tests in the “pile cap, pile, ground” system are presented in the article. It is shown that the waves transmitted across the boundary between a pile cap and pile are sequential and not in the form of a single pulse. If there are two or more piles in the “pile cap–pile–ground” system the signal response above the test pile will be “noisy” by reflections from neighboring piles. The possible options for performing measurements in case of lack of access to the pile head (the presence of a pile cap) are described in detail. Information about the location of the sensor and striking to wave generation is given. The construction of the new sensor which allows to measure on the side surface of the pile without creating a horizontal platform on the pile is briefly described. Examples of various objects with studied piles united by a cap are given. The investigated objects have a pile caps of various designs: continuous footing, pad, and slab foundation. On the graphics obtained as a result of measurement reflections from the pile toe are clearly identified. It has been practically shown that by using the method of filtering and comparing signals response on the test pile it is possible to control the length of piles located under the pile cap of various types and construction.