Crohn's disease (CD) is a chronic inflammatory bowel disorder caused by environmental and genetic factors. The purpose of this study was to analyse the possible influence of functional variants of genes of OCTN cation transporters on the carnitine ester profile of patients with CD. Genotyping for SLC22A4 1672C → T, SLC22A5-207G → C mutations and three common NOD2 variants (R702W, G908R and 1007finsC) were performed in 100 adult CD patients and in ninety-four healthy controls by direct sequencing. The carnitine ester profile was determined using ESI triple quadrupole tandem MS. Contrary to the NOD2/CARD15 mutations, none of the SLC variants showed increased prevalence in the CD group, the prevalence of TC haplotype did not differ between the patients and the controls. In the mixed group of CD patients the fasting propionyl- (0·243 (sem 0·008) v. 0·283 (sem 0·014) μmol/l), butyryl- (0·274 (sem 0·009) v. 0·301 (sem 0·013)) and isovalerylcarnitine (0·147 (sem 0·006) v. 0·185 (sem 0·009)) levels were decreased; while the level of octenoyl- (0·086 (sem 0·006) v. 0·069 (sem 0·005)), myristoleyl- (0·048 (sem 0·003) v. 0·037 (sem 0·003)), palmitoyl- (0·140 (sem 0·005) v. 0·122 (sem 0·004)) and oleylcarnitine (0·172 (sem 0·006) v. 0·156 (sem 0·008); P < 0·05 in all comparisons) were increased. After sorting the patients into SLC22A genotype-specific subgroups, no significant differences could be observed between them. The carnitine ester profile data suggest selective involvement of the carnitine esters in CD patients, probably due to their altered metabolism.