Antrochoanal polyp (ACP) is a soft tissue mass originating from the maxillary antrum, emerging from the ostium and extending to the choana through the nasal cavity. Our aim was to investigate the light microscopic and ultrastructural features of ACP and to compare these with nasal polyps originating from the middle meatus (MMP). Seven ACP and seven MMP specimens were evaluated by transmission electron microscopy (TEM) and light microscopy. TEM examination showed epithelial cells with intact cilia covering both polyps. In some MMP cases, degeneration of the epithelium associated with some cilia loss was noted. Goblet cell hyperplasia was more prominent in MMP cases. Degeneration and partial destruction of the endothelial cells of the blood vessels were common findings in ACP cases; however, in the MMP group, endothelial cells were mostly intact with a few aggregates of ribosomes, and intact cell junctions were noted. Light microscopic examination revealed that inflammatory cells in the ACP group were numerous. However, eosinophils were predominant in MMP cases. Squamous metaplasia of the surface epithelium was detected in five ACP cases, but in none of the MMP cases. Basement membrane thickening was detected in two cases of the ACP and in four cases of the MMP group. There was a statistically significant difference between the two groups for inflammatory cells, eosinophilic cell infiltration, squamous cell metaplasia, endothelial cell destruction and goblet cell metaplasia. In conclusion, the low number of eosinophils, the high number of other inflammatory cells, the normal appearing basement membrane and intact and normal surface epithelium may reveal that the etiology of ACP might arise from chronic inflammatory processes rather than allergy. The destruction of the endothelium may be considered as a further sign of chronic inflammation.