Cytauxzoon felis typically causes fatal disease in domestic cats. Survival after infection and persistent parasitemia without clinical illness has been documented in a few cases. To our knowledge there are no prevalence studies of C. felis in domestic cats. The purpose of this study was to estimate the prevalence of C. felis infected cats that were presented to trap-neuter-return programs in Florida, North Carolina and Tennessee. Cats that were presented to trap-neuter-return programs were tested using a C. felis-specific PCR assay. A total of 961 domestic cats were tested (494 from Florida; 392 from North Carolina; 75 from Tennessee). Prevalence of C. felis infection in this population was 0.3%. Two cats from Florida and one cat from Tennessee tested positive for the presence of C. felis DNA. These amplicons were sequenced and confirmed to be C. felis. The cat from Tennessee was alive without evidence of illness 2 months post-surgery. The other two cats were alive 24 h post-surgery, but were then lost to follow-up. This is the first report documenting C. felis infections in free-roaming cats. Despite the low prevalence rate, the presence of apparently healthy infected free-roaming cats suggests that they may have the capacity to serve as an additional reservoir host for C. felis. Further investigations should evaluate the potential vector competence of domestic cats as well as the role of chronically infected cats in areas in which cytauxzoonosis appears hyperendemic.