The expression of the Elovl3 gene, which belongs to the Elovl gene family coding for microsomal enzymes involved in very long chain fatty acid (VLCFA) elongation, is dramatically increased in mouse brown adipose tissue upon cold stimulation. In the present study we show that the cold induced Elovl3 expression is under the control of the peroxisome proliferator-activated receptor (PPAR), and that this regulation is part of a fundamental divergence in the regulation of expression for the different members of the Elovl gene family. In cultured brown adipocytes, a mixture of norepinephrine, dexamethasone and the PPAR ligand Wy-14643, which rendered the adipocytes a high oxidative state, was required for substantial induction of Elovl3 expression while the same treatment suppressed Elovl1 mRNA levels. The nuclear liver X receptor (LXR) have been implicated in the control of fatty acid synthesis and subsequent lipogenic processes in several tissues. This regulation is also exerted in part by sterol regulatory element-binding protein (SREBP-1), which is a target gene of LXR. We found that the stimulation of Elovl3 expression was independent of LXR and SREBP-1 activation. In addition, exposure to the LXR agonist TO901317 increased nuclear abundance of LXR and mature SREBP-1 as well as the expression of the elongases Lce and Elovl1 in a lipogenic fashion, but repressed Elovl3 expression. A functional consequence of this was seen on the level of esterified saturated fatty acids, such as C22:0, which was coupled to Elovl3 expression. These data demonstrate differential transcriptional regulation and concomitantly different functional roles for fatty acid elongases in lipid metabolism of brown adipocytes, which reflects the metabolic status of the cells.