Feline infectious peritonitis (FIP) is a fatal disease for which no simple antemortem diagnostic assay is available. A new polymerase chain reaction (PCR) test has recently been developed that targets the spike protein region of the FIP virus (FIPV) and can identify specific mutations (M1030L or S1032A), the presence of which indicates a shift from feline enteric coronavirus (FeCV) to FIPV. This test will only be useful in the geographical region of interest, however, if the FIP viruses contain these mutations. The primary objective of this study was to determine the presence of the M1030L or S1032A mutations in FeCV derived from stool samples from a selected group of healthy cats from households and shelters and determine how many of these cats excrete FeCV. The secondary objective was to evaluate how often these specific FIPV mutations were present in tissue samples derived from cats diagnosed with FIP at postmortem examination. Feline enteric coronavirus (FeCV) was detected in 46% of fecal samples (86/185), all were FeCV type 1, with no difference between household or shelter cats. Only 45% of the FIPV analyzed contained the previously reported M1030L or S1032A mutations. It should be noted that, as the pathological tissue samples were opportunistically obtained and not specifically obtained for PCR testing, caution is warranted in interpreting these data.