Periweaning Failure to Thrive Syndrome (PFTS) is a serious and potentially fatal disorder with variable morbidity and mortality rates that have been reported in US and Canadian farms. A genetic basis has been hypothesized. To investigate what regions of the genome could be linked to that, a total of 70 affected and 37 non-affected piglets were genotyped with over 60,000 genetic markers to investigate genetic differences between the two groups. This allows for the identification of genomic regions that could be linked to resistance to the disease providing new insights and knowledge on the genetic basis of this syndrome.