Sarcocystis hominis, one of the three species of Sarcocystis that cause muscular cysts in cattle, is a protozoan parasite that can infect the human intestinal tract. The objective of the present study was to develop a new molecular identification method capable of discriminating among the bovine Sarcocystis species and to apply this tool in combination with stereomicroscopy to determine the presence of Sarcocystis spp. in minced beef in Belgium, with special attention to Sarcocystis hominis. A PCR technique based on the 18S rRNA sequence and by sequencing of the amplicon was highly specific. Sequence analysis of PCR products from thick-walled cysts collected from minced beef in Belgium revealed that S. hominis was present in 97.4% of the samples. Because the consumption of raw minced beef is common in Belgium and certain other European countries, these findings may point to an underestimated risk to public health.