Capillaria aerophila, a trichuroid nematode causing pulmonary infections in wild and domestic carnivores, is occasionally and potentially poorly recognized in infections of humans due to clinicopathological mimicry and a lack of accurate, robust laboratory diagnostics. The present work evaluated the efficiency of a DNA-based assay amplifying a partial cytochrome c oxidase subunit 1 (cox1) gene of C. aerophila in the diagnosis of lung capillariosis. Fecal samples from 34 dogs and 10 cats positive at parasitological examination for C. aerophila and other endoparasites (i.e., other lungworms, whipworms, roundworms, hookworms, tapeworms, and/or coccidia) and from 44 animals negative for C. aerophila but positive for other endoparasites were molecularly examined. Of the 44 samples positive for C. aerophila at copromicroscopy, 43 scored positive (i.e., 33/34 dogs and 10/10 cats) in seminested PCR, resulting in a sensitivity of 97 to 100%. Samples that were copromicroscopy negative for C. aerophila although positive for other endoparasites never produced a PCR product or nonspecific amplicons. The specific PCR amplification of C. aerophila (i.e., specificity of 100%) was confirmed by a nucleotide sequence analysis of the cox1 amplicons. The potential implications of the molecular diagnosis of lung capillariosis are discussed.