Most deletions in chromosome 1p36 are new mutations, that occur before fertilization, during the formation of gametes (eggs or sperm). Chromosome abnormalities usually occur when there is an error in cell division. There are two kinds of cell division and they are mitosis and meiosis. Meiosis is the cell division relating to reproduction. Meiosis results in cells with half the number of chromosomes, 23 instead of the normal 46. These are the eggs and sperm. Errors can occur when the chromosomes are being duplicated. There have been reports of patients with 1p36 deletion syndrome whose parents have a balanced translocation. This is when a portion of one chromosome is transferred to another chromosome. This means that the parent has the "36" portion of chromosome 1 attached to another chromosome. Then what happens (for the child to have the deletion) is when the chromosome is copied, the child's chromosome 1 has the same "36" piece missing. Instead of it being "translocated" the piece is just missing, it is not attached to another chromosome like the parents' is.  The mechanism causing chromosome breakage is unknown.

Deletions of parental origin (from the father) are larger than the deletions deriving from the maternal (mother) chromosome. The majority of deletions are maternally derived.  There doesn't seem to be differences in the clinical manifestations (the symptoms or observable conditions which are seen as a result of 1p36) based on whether the deletion is on the paternal or maternal chromosome.