Peroxisomes are no longer regarded as autonomous organelles because evidence for their interplay with other cellular organelles is emerging. Peroxisomes interact with mitochondria in several metabolic pathways, including beta-oxidation of fatty acids and the metabolism of reactive oxygen species. Both organelles are in close contact with the endoplasmic reticulum (ER) and share several proteins, including organelle fission factors. Today, the study of peroxisome biogenesis disorders mainly focuses on metabolic defects such as accumulation of very long chain fatty acids or plasmalogen deficiency. In addition to metabolic dysregulation, mitochondria and ER abnormalities have also been observed. Whether these contribute to disease pathology is not yet known, but recent findings suggest that this possibility should be considered. Here, we discuss the potential involvement of organelle interplay in peroxisomal disorders.