Perilipins are lipid droplet-coating proteins that regulate intracellular lipolysis in adipocytes. A haplotype of two perilipin gene (PLIN) single nucleotide polymorphisms, 13041A>G and 14995A>T, has been previously associated with obesity risk. Furthermore, the available data indicate that this association may be modified by sex. We hypothesized that this haplotype would associate with body fatness, aerobic fitness, and a number of cardiovascular (CV) risk factor phenotypes before and after a 6-mo endurance exercise training program in sedentary older Caucasians. The major haplotype group (13041A/14995A; n = 57) had significantly lower body mass index (BMI) and body fatness compared to non-carriers of the AA haplotype (n = 44) before the training intervention. Training improved body composition in both groups, but fatness remained higher in non-carriers than AA carriers after training. This fat retention in non-carriers blunted their maximal oxygen uptake (VO₂max) adaptation to training. Female non-carriers had substantially higher concentrations of several conventionally- and NMR-measured HDL-C subfractions than male non-carriers before and after training, but only minimal differences were found between the sexes in the AA haplotype group. Haplotype group differences in baseline and after-training responses to an oral glucose tolerance test (OGTT) also differed by sex, as non-carrier men had the highest baseline area under the insulin curve (insulin AUC), but were the only group to significantly improve insulin AUC with training. The insulin sensitivity index and plasma glucose responses to the OGTT were more favorable in AA carriers than non-carriers before and after training. Overall, our findings suggest that PLIN variation explains some of the interindividual differences in the response of obesity and CV phenotypes to exercise training. Further, these data contribute to the growing understanding of PLIN as a candidate gene for human obesity and the cardiometabolic consequences of excess adiposity.