Between 2004 and 2008, 338 samples from 156 German turkey, chicken, and peacock flocks with suspected histomonosis (histomoniasis) were sent to the Institute for Poultry Diseases of the Free University Berlin. Most samples were from ceca or livers; the other samples were organ pools or were taken from other organs or the environment. In 108 samples from 65 flocks, histomonal DNA was detected by polymerase chain reaction (PCR). Tetratrichomonas gallinarum DNA was found in 5.3% of investigated samples from flocks infected with Histomonas meleagridis and in 27.4% of investigated samples from flocks that were not infected with H. meleagridis. For subtyping of the strains, the C-profiling method, a method used to analyze the internal transcribed spacer-1 (ITS-1) of the rRNA gene, was modified to be more specific for H. meleagridis. Results showed the presence of more than the three subtypes described so far. There was no clear correlation between the subtype and the host. By C-profiling the clonal cultures, heterogeneous ITS-1 sequences were shown to probably result from intragenomic differences between rRNA genes.