Abstract. The purpose of the current study was to compare the molecular detection rate of Lawsonia intracellularis between feces and rectal swabs collected from 42 foals with suspected equine proliferative enteropathy (EPE). Fecal samples and rectal swabs were processed for DNA purification by using an automated extraction system. The purified DNA was then analyzed by real-time polymerase chain reaction (PCR) for the presence of the aspartate ammonia lyase (aspA) gene of L. intracellularis. Absolute quantitation was calculated by using a standard curve for L. intracellularis and expressed as copy numbers of the aspA gene of L. intracellularis per microliter of purified DNA. The combined PCR detection rate for L. intracellularis was 90%, with 38 foals testing PCR positive in feces (33 samples), rectal swabs (32), or both (27). Six foals tested PCR positive only in feces, whereas 5 tested positive only in rectal swabs. Feces yielded a significantly higher aspA gene copy number of L. intracellularis than rectal swabs. Feces and rectal swabs tested PCR negative from 4 foals. In conclusion, the results showed that feces yielded similar numbers of PCR-positive results, with a higher L. intracellularis aspA gene load than rectal swabs. By analyzing dual samples, the PCR detection rate for L. intracellularis increased from 76% and 79% for rectal swabs and feces, respectively, to 90%. Rectal swabs should be considered as an alternative sample type for EPE-suspected patients with decreased or no fecal output.Key words: Equine proliferative enteropathy; feces; horses; Lawsonia intracellularis; real-time polymerase chain reaction; rectal swab.Equine proliferative enteropathy (EPE) is a disease of foals caused by the obligate intracellular organism Lawsonia intracellularis. This emerging disease affects weanling foals and causes fever, lethargy, peripheral edema, diarrhea, colic, and weight loss. 6 The antemortem diagnosis of EPE may be challenging and relies on the presence of hypoproteinemia, exclusion of common enteric diseases, thickening of segments of the small intestinal wall observed on abdominal ultrasonography, positive serology, and molecular detection of L. intracellularis in feces. 8 One must keep in mind that a positive serologic result may represent exposure to infection rather than disease. Although no commercially available serologic assay has yet been systematically evaluated for the equine species, serologic assays have proven useful for routine diagnosis of PE in horses when combined with clinical signs and molecular detection of L. intracellularis in feces. 7,14 Several polymerase chain reaction (PCR) assays have been developed for the detection of L. intracellularis in feces. The sensitivity and specificity of the PCR technique in fecal samples has been evaluated for pigs and showed variable sensitivity and consistently high specificity. 3,5,9,13 Sensitivity is affected by sample quality and the presence of inhibitory substances in feces. PCR appears to reliably demonstrate L. intracellularis in the fec...