Hungary’s deepest borehole, Hód-I, was drilled in 1969–71 SE of the town of Hódmezővasarhely, in order to explore one of the thickest Neogene basin fills of the entire Pannonian Basin (the Makó Trough). The final depth of the well was 5842.5 m. According to earlier analyses of 45 core samples taken from the borehole, the lowermost 700 m was thought to belong to the Middle Miocene (Badenian and, possibly, Sarmatian Stages), whereas the overlying part was believed to belong to the Upper Miocene (deposits of Lake Pannon, Pannonian Stage), Pliocene, and Quaternary. In order to establish a more precise position of the Neogene stage boundaries, we carried out micropaleontological investigations on the 4100 to 5823 m interval (cores 25 to 45). Ostracods have been prepared by solution of the samples in acetic acid. Dinoflagellates were investigated in palynological preparations and in petrographic thin sections. It was found that core 34 (5070–5074 m), earlier thought to represent the base of the Pannonian Stage, in fact belongs to the younger part of the Lake Pannon sequence (Spiniferites validus Zone). Downwards to the base of the borehole, the Spiniferites paradoxus, Pontiadinium pecsvaradensis, and Spiniferites bentorii oblongus Zones were found, all belonging to the Pannonian. Accordingly, ostracods indicated the younger part of the Upper Miocene lacustrine sequence for the upper samples of the investigated interval, and older Upper Miocene down to core 44. Thus, the drilling failed to reach the base of the Pannonian Stage. The huge thickness (>6 km) of the postrift sediments above the relatively thin synrift stages (Badenian and ?Sarmatian) in the Makó Trough corroborates the notion that simple rifting models are not sufficient to adequately describe basin evolution in the central part of the Pannonian Basin.