Obesity and related disorders have become a major health problem. Understanding the interaction between genetic and environmental factors influencing the susceptibility to develop obesity is important when pinpointing people at risk. In a longitudinal study of 256 non-obese adolescents, the influence of the insulin gene (INS) variable number of tandem repeats (VNTR) on anthropometric measures and fat mass was investigated. The adolescents were examined at the age of 12.4 (2.3) (mean, SD) and 16.2 (2.3) years, and at follow-up with dual x-ray absorptiometry (DXA) for measurement of body composition. INS VNTR classes I and III alleles were investigated using the -23T/A single nucleotide polymorphism as a surrogate marker. There was a non-significant trend towards increased body mass index (BMI) and fat mass with the class III allele in girls. Homozygotes for the INS VNTR class III allele had a greater increase in BMI compared with those that were homozygous or heterozygous for the class I allele (3.8 (1.6) versus 2.4 (1.9) kg/m2, p = 0.03), and they had higher fat mass (36.4 (3.9) versus 31.3 (6.8)%, p = 0.02) at follow-up. Our finding that homozygosity of the INS VNTR class III allele seems to predispose to increased weight gain and fat mass raises the possibility that this genotype may be one of the important factors in the gene-environment interaction that eventually results in overweight and insulin resistance.