The relationships between levels of skatole and androstenone in fat, plasma levels of skatole metabolites, plasma testosterone and estrone sulfate, and levels of cytochrome P450IIE1 in liver were investigated in Swedish Yorkshire pigs and F4 Wild Pig crosses. Levels of skatole, the skatole metabolite MIII, and androstenone were higher in males from the Wild Pig crosses than in the Yorkshire pigs. Plasma levels of the skatole metabolite MII and the ratio between MII and MIII were higher in female Yorkshire pigs than in male pigs. Skatole was correlated with androstenone, cytochrome P450IIE1, and estrone sulfate in the Wild Pig crosses but not in Yorkshire pigs. However, plasma levels of skatole metabolites were not correlated to levels of cytochrome P450IIE1 in liver in either group on animals. Pigs with high levels of cytochrome P450IIE1 in liver had low levels of skatole in fat, and pigs with low levels of cytochrome P450IIE1 in liver had low and high skatole levels. Using stepwise regression analysis, only levels of cytochrome P450IIE1 in liver significantly explained the variation in skatole levels in the Wild Pig crosses. Our results support the hypothesis that low levels of cytochrome P450IIE1 in liver may result in high levels of skatole in backfat of uncastrated male pigs due to decreased metabolism and clearance of skatole. However, these pigs cannot be identified based on plasma levels of skatole metabolites MII and MIII.