Abstract The paper presents the method of the three-dimensional reconstruction of biological objects’ internal structure heterogeneity based on the ultrasonic examination of a woman’s breast biopsy phantom. The phantom is made of quasi-homogeneous dense gel in which drops of lesions, characterized by fixed sizes and two different acoustic impedances, were dipped at random. For the purpose of this research a special measurement setup was elaborated, enabling a non-invasive in vitro imaging of biological objects’ internal structure in cross-sections for fixed levels, by means of ultrasound transmission tomography (UTT) using the parallel-ray projection geometry of scanning. The two-dimensional images of the local values of ultrasonic wave’s propagation velocity in the phantom’s internal structure (ultrasonic tomograms) were reconstructed for fixed levels (by using the convolution and back-projection algorithm) from the measurements of average values of ultrasonic signals’ runtime propagated from many directions around the object dipped in water. Analyzing the values of particular pixels and using an appropriate image processing technique, in effect the three-dimensional image of heterogeneity boundaries in the examined phantom’s internal structure was computer-reconstructed. The obtained results are compatible with the specification provided by the phantom’s producer in terms of sizes and acoustic parameters of lesions, which can simulate pathological changes and of the gel imitating the healthy tissue. It means that the method presented, after an appropriate modification and development of the measurement setup with an aim to accelerate the object scanning process and thus provide an opportunity for non-invasive in vivo examinations, could be applied for detecting and diagnosing tumors in women’s breasts.