In mammals, obesity, together with other physical traits, is known to be associated with leptin, a hormone encoded by the LEP gene and secreted by White adipocytes in response to changes in body weight and energy. By extracting DNA from hair follicles and employing the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism technique, the associations of LEP gene polymorphisms A1112G and T3469C with body length, backfat thickness, adjusted backfat thickness, average daily gain, and weight of 103 sows, and birth weight, weaning weight, and average daily gain of 153 piglets from a Philippine government-accredited breeder farm, were analyzed. Very low frequencies of the AA genotype (0.013–0.039) for A1112G and the CC genotype (0.007–0.097) for T3469C were computed for all sample sows and piglets. Hence, selection against these genotypes can be inferred. For the association analysis, no association was found between any of the LEP gene genotypes and the traits in sample sows and piglets. However, non-genetic factors such as breed and parity were shown to interact with the A1112G genotypes and affect weight and average daily gain in sample sows. Landrace and Large White sows with AG and GG genotypes were heavier than those with the AA genotypes. Also, the AG individuals having one to two parities have lower average daily gain than those with already three to four parities. Results of this study can be of help in breeding programs especially in selection programs and improvement of management techniques in farms.