Laminitis remains a poorly understood form of lameness in the horse despite being heavily researched. Endocrinopathic laminitis is an insidious form of laminitis that often results from insulin resistance (an indicator of Equine Metabolic Syndrome or EMS) or equine pituitary pars intermedia dysfunction (PPID). Both conditions occur in older horses with PPID having a later age of onset than EMS and horses are often characterized as having a "cresty" neck. EMS horses have persistent hyperinsulinemia while horses affected by PPID have elevated ACTH levels. Though no specific genetic predispositions have been identified for EMS or PPID, ponies are frequently observed to have both conditions. The objective of this study was to conduct a genome-wide association to identify candidate genes that may predispose individuals to EMS, PPID or both. A total of 65 horses, at least ten years old and of full or majori ty Arabian descent were divided into four categories based on previous endocrinology testing. Horses with ACTH levels greater than 70 pg/mL and insulin levels less than 40 uIU/mL were designated "PPID" while horses with insulin levels > 70 uIU/mL and ACTH levels less than 40 pg/mL were designated "EMS". Horses with ACTH and insulin levels < 40 pg/mL or uIU/mL, respectively, were considered "Normal" and those with both levels > 70 were grouped into the fourth category termed "Both". The Illumina Infinium® II Assay (Illumina Inc, San Diego, CA, USA) was performed on the EquineSNP 50 Genotyping BeadChip (Illumina Inc, San Diego, CA, USA) using DNA extracted from tail hair or blood samples. Data was analyzed using the PLINK v1.07 Whole genome association analysis toolset and JMP 8.0 (SAS Insitute Inc, Cary, NC, USA). Basic association (chi-square) tests were used to compare various groupings of disease cases and controls for a total of 15 qualitative associations. Quantitative associations were also performed for highest recorded ACTH (excluding August -October measurements) and insulin levels. An additional association was performed comparing horses with at least one episode of laminitis versus those with no recorded history of laminitis, regardless of disease cat egory. SNPs with a missing genotype rate greater than 10% were excluded from analysis. SNPs in linkage disequilibrium (r2 > 0.99) were pruned to a single SNP per haplotype block in all graphs. Any SNPs exceeding the Bonferroni [alpha] threshold were mapped on the UCSC Genome Browser using the September 2007 assembly (EquCab2.0) of the horse genome. Candidate genes were identified within ~50 kb of each significant SNP. A total of 68 SNPs representing 59 different loci exceeded the significance threshold after corr ection for multiple testing. The most significant SNP, BIEC2-215377 (ECA 13) with a P-value of 4.34 e-7, was identified in the quantitative association with the highest ACTH level recorded for each individual. This SNP yielded one candidate gene, XPO6. Other SNPs that did not exceed the significance threshold but did vary from their expected P-value in a quantile-quantile plot include BIEC2 -770354 (ECA3) and its neighboring SNP in linkage disequilibrium, BIEC2 -770355 which yielded two candidate genes, FTO and ATP5H. This study resulted in the discovery of several good candidate genes that are worthy of fine mapping. However, epistatic effects may hamper the ability to identify all genetic predispositions. Improvements in diagnostic testing may allow for more specific classification of disease categories and refinement of the current data set. The present study is also limited by the relatively limited coverage of the Equine SNP50 chip. Expanded platforms with better coverage may allow for the discovery of more candidate genes.